diff --git a/apps/backend/backend_commit.c b/apps/backend/backend_commit.c
index fb4d2fa0..0a967473 100644
--- a/apps/backend/backend_commit.c
+++ b/apps/backend/backend_commit.c
@@ -134,6 +134,63 @@ generic_validate(clixon_handle       h,
     goto done;
 }
 
+/*! Given a transaction src/target, compute diffs and set flags
+ *
+ * @param[in]  h       Clixon handle
+ * @param[in]  td      Transaction data
+ * @retval     0   OK
+ * @retval    -1   Error
+ */
+static int
+compute_diffs(clixon_handle       h,
+              transaction_data_t *td)
+{
+    int    retval = -1;
+    int    i;
+    cxobj *xn;
+
+    /* Clear flags xpath for get */
+    xml_apply0(td->td_src, CX_ELMNT, (xml_applyfn_t*)xml_flag_reset,
+               (void*)(XML_FLAG_MARK|XML_FLAG_CHANGE));
+    /* 3. Compute differences */
+    if (xml_diff(td->td_src,
+                 td->td_target,
+                 &td->td_dvec,      /* removed: only in running */
+                 &td->td_dlen,
+                 &td->td_avec,      /* added: only in candidate */
+                 &td->td_alen,
+                 &td->td_scvec,     /* changed: original values */
+                 &td->td_tcvec,     /* changed: wanted values */
+                 &td->td_clen) < 0)
+        goto done;
+    if (clixon_debug_get() & CLIXON_DBG_DETAIL)
+        transaction_dbg(h, CLIXON_DBG_DETAIL, td, __FUNCTION__);
+    /* Mark as changed in tree */
+    for (i=0; i<td->td_dlen; i++){ /* Also down */
+        xn = td->td_dvec[i];
+        xml_flag_set(xn, XML_FLAG_DEL);
+        xml_apply(xn, CX_ELMNT, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_DEL);
+        xml_apply_ancestor(xn, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_CHANGE);
+    }
+    for (i=0; i<td->td_alen; i++){ /* Also down */
+        xn = td->td_avec[i];
+        xml_flag_set(xn, XML_FLAG_ADD);
+        xml_apply(xn, CX_ELMNT, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_ADD);
+        xml_apply_ancestor(xn, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_CHANGE);
+    }
+    for (i=0; i<td->td_clen; i++){ /* Also up */
+        xn = td->td_scvec[i];
+        xml_flag_set(xn, XML_FLAG_CHANGE);
+        xml_apply_ancestor(xn, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_CHANGE);
+        xn = td->td_tcvec[i];
+        xml_flag_set(xn, XML_FLAG_CHANGE);
+        xml_apply_ancestor(xn, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_CHANGE);
+    }
+    retval = 0;
+ done:
+    return retval;
+}
+
 /*! Common startup validation
  *
  * Get db, upgrade it w potential transformed XML, populate it w yang spec,
@@ -168,7 +225,6 @@ startup_common(clixon_handle       h,
     int                 ret;
     modstate_diff_t    *msdiff = NULL;
     cxobj              *xt = NULL;
-    cxobj              *x;
     cxobj              *xret = NULL;
     cxobj              *xerr = NULL;
 
@@ -181,7 +237,7 @@ startup_common(clixon_handle       h,
             goto done;
     /* Add system-only config to running */
     if (clicon_option_bool(h, "CLICON_XMLDB_SYSTEM_ONLY_CONFIG")){
-        if ((ret = xmldb_get0(h, "running", YB_MODULE, NULL, "/", 0, 0, &xt, NULL, NULL)) < 0)
+        if ((xt = xml_new(DATASTORE_TOP_SYMBOL, NULL, CX_ELMNT)) == NULL)
             goto done;
         if (xmldb_system_only_config(h, "/", NULL, &xt) < 0)
             goto done;
@@ -301,17 +357,17 @@ startup_common(clixon_handle       h,
     /* Apply default values (removed in clear function) */
     if (xml_default_recurse(xt, 0, 0) < 0)
         goto done;
-
     /* Handcraft transition with with only add tree */
     td->td_target = xt;
     xt = NULL;
-    x = NULL;
-    while ((x = xml_child_each(td->td_target, x, CX_ELMNT)) != NULL){
-        xml_apply0(x, CX_ELMNT, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_ADD);
-        if (cxvec_append(x, &td->td_avec, &td->td_alen) < 0)
-            goto done;
-    }
-
+    /* Add global src defaults. */
+    if (xml_global_defaults(h, td->td_src, NULL, NULL, yspec, 0) < 0)
+        goto done;
+    /* Apply default values (removed in clear function) */
+    if (xml_default_recurse(td->td_src, 0, 0) < 0)
+        goto done;
+    if (compute_diffs(h, td) < 0)
+        goto done;
     /* 4. Call plugin transaction start callbacks */
     if (plugin_transaction_begin_all(h, td) < 0)
         goto done;
@@ -496,8 +552,6 @@ validate_common(clixon_handle       h,
 {
     int         retval = -1;
     yang_stmt  *yspec;
-    int         i;
-    cxobj      *xn;
     int         ret;
 
     if ((yspec = clicon_dbspec_yang(h)) == NULL){
@@ -524,43 +578,8 @@ validate_common(clixon_handle       h,
         goto done;
     if (ret == 0)
         goto fail;
-    /* Clear flags xpath for get */
-    xml_apply0(td->td_src, CX_ELMNT, (xml_applyfn_t*)xml_flag_reset,
-               (void*)(XML_FLAG_MARK|XML_FLAG_CHANGE));
-    /* 3. Compute differences */
-    if (xml_diff(td->td_src,
-                 td->td_target,
-                 &td->td_dvec,      /* removed: only in running */
-                 &td->td_dlen,
-                 &td->td_avec,      /* added: only in candidate */
-                 &td->td_alen,
-                 &td->td_scvec,     /* changed: original values */
-                 &td->td_tcvec,     /* changed: wanted values */
-                 &td->td_clen) < 0)
+    if (compute_diffs(h, td) < 0)
         goto done;
-    if (clixon_debug_get() & CLIXON_DBG_DETAIL)
-        transaction_dbg(h, CLIXON_DBG_DETAIL, td, __FUNCTION__);
-    /* Mark as changed in tree */
-    for (i=0; i<td->td_dlen; i++){ /* Also down */
-        xn = td->td_dvec[i];
-        xml_flag_set(xn, XML_FLAG_DEL);
-        xml_apply(xn, CX_ELMNT, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_DEL);
-        xml_apply_ancestor(xn, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_CHANGE);
-    }
-    for (i=0; i<td->td_alen; i++){ /* Also down */
-        xn = td->td_avec[i];
-        xml_flag_set(xn, XML_FLAG_ADD);
-        xml_apply(xn, CX_ELMNT, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_ADD);
-        xml_apply_ancestor(xn, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_CHANGE);
-    }
-    for (i=0; i<td->td_clen; i++){ /* Also up */
-        xn = td->td_scvec[i];
-        xml_flag_set(xn, XML_FLAG_CHANGE);
-        xml_apply_ancestor(xn, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_CHANGE);
-        xn = td->td_tcvec[i];
-        xml_flag_set(xn, XML_FLAG_CHANGE);
-        xml_apply_ancestor(xn, (xml_applyfn_t*)xml_flag_set, (void*)XML_FLAG_CHANGE);
-    }
     /* 4. Call plugin transaction start callbacks */
     if (plugin_transaction_begin_all(h, td) < 0)
         goto done;
diff --git a/example/main/example_backend.c b/example/main/example_backend.c
index 7ad1241e..98c76f1c 100644
--- a/example/main/example_backend.c
+++ b/example/main/example_backend.c
@@ -260,13 +260,13 @@ main_commit(clixon_handle    h,
     size_t  len;
     cvec   *nsc = NULL;
 
+    if (_transaction_log)
+        transaction_log(h, td, LOG_NOTICE, __FUNCTION__);
     if (_system_only_xpath != NULL){
         if (main_system_only_commit(h, td) < 0)
             goto done;
         goto ok;
     }
-    if (_transaction_log)
-        transaction_log(h, td, LOG_NOTICE, __FUNCTION__);
     if (_validate_fail_xpath){
         if (_validate_fail_toggle==1 &&
             xpath_first(transaction_target(td), NULL, "%s", _validate_fail_xpath)){
diff --git a/test/test_datastore_system_only.sh b/test/test_datastore_system_only.sh
index bf8a56ca..42b8ae20 100755
--- a/test/test_datastore_system_only.sh
+++ b/test/test_datastore_system_only.sh
@@ -24,6 +24,9 @@ AUTOCLI=$(autocli_config clixon-\* kw-nokey false)
 # Define default restconfig config: RESTCONFIG
 RESTCONFIG=$(restconf_config none false)
 
+flog=$dir/backend.log
+touch $flog
+
 cat <<EOF > $cfg
 <clixon-config xmlns="http://clicon.org/config">
   <CLICON_FEATURE>ietf-netconf:startup</CLICON_FEATURE>
@@ -235,6 +238,37 @@ function check_db()
     fi
 }
 
+# Check statements in log
+# arg1: a statement to look for (eg "0 main_commit")
+# arg2: expected line number
+function checklog(){
+    s=$1 # statement
+    l0=$2 # linenr
+
+    new "Check $s in log"
+    echo "grep \"transaction_log $s line:$l0\"  $flog"
+    t=$(grep -n "transaction_log $s" $flog)
+    if [ -z "$t" ]; then
+        echo -e "\e[31m\nError in Test$testnr [$testname]:"
+        if [ $# -gt 0 ]; then
+            echo "Not found \"$s\" on line $l0"
+            echo
+        fi
+        echo -e "\e[0m"
+        exit -1
+    fi
+    l1=$(echo "$t" | awk -F ":" '{print $1}')
+    if [ $l1 -ne $l0 ]; then
+        echo -e "\e[31m\nError in Test$testnr [$testname]:"
+        if [ $# -gt 0 ]; then
+            echo "Expected match on line $l0, found on $l1"
+            echo
+        fi
+        echo -e "\e[0m"
+        exit -1
+    fi
+}
+
 new "test params: -f $cfg"
 
 if [ $BE -ne 0 ]; then
@@ -396,13 +430,16 @@ sudo cp $dir/x_db_xml $dir/startup_db
 sudo cp $dir/y_db $dir/system-only.xml
 
 if [ $BE -ne 0 ]; then
-    new "start backend -s startup -f $cfg -- -o store/keys/key/system-only-data -O $dir/system-only.xml"
-    start_backend -s startup -f $cfg -- -o store/keys/key/system-only-data -O $dir/system-only.xml
+    # -t means transaction logging, -o/-O means system-only-config
+    new "start backend -s startup -f $cfg -l f$flog -- -t -o store/keys/key/system-only-data -O $dir/system-only.xml"
+    start_backend -s startup -f $cfg -l f$flog -- -t -o store/keys/key/system-only-data -O $dir/system-only.xml
 fi
 
 new "wait backend 3"
 wait_backend
 
+checklog '0 main_commit add: <normal-data>otherdata</normal-data>' 7
+
 new "Get mydata from running after startup"
 expecteof_netconf "$clixon_netconf -qf $cfg" 0 "$DEFAULTHELLO" "<rpc $DEFAULTNS><get-config><source><running/></source></get-config></rpc>" "<rpc-reply $DEFAULTNS><data><store xmlns=\"urn:example:std\"><keys><key><name>a</name><system-only-data>mydata</system-only-data><normal-data>otherdata</normal-data></key></keys></store></data></rpc-reply>"