diff --git a/webapp/TargetedMS/js/QCPlotHelperBase.js b/webapp/TargetedMS/js/QCPlotHelperBase.js
index 11fb334b3..c616b8d2e 100644
--- a/webapp/TargetedMS/js/QCPlotHelperBase.js
+++ b/webapp/TargetedMS/js/QCPlotHelperBase.js
@@ -332,21 +332,17 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
 
                         Ext4.Object.each(this.guideSetDataMap, function(guideSetId, guideSetData) {
                             // for truncating out of range guideset data  find first index of plotDate ending at guideset.trainingEnd
-                            if (plotData.guideSetId === guideSetId && plotData.inGuideSetTrainingRange && guideSetData.TrainingEnd <= this.startDate) {
+                            if (plotData.guideSetId == guideSetId && plotData.inGuideSetTrainingRange && guideSetData.TrainingEnd <= this.startDate) {
                                 this.filterPoints[frag][plotData.MetricId]['filterPointsFirstIndex'] = j + 1;
-                                // ReferenceRangeSeries is used to separate series
                                 plotData['ReferenceRangeSeries'] = "GuideSet";
                             }
-                            else {
-                                plotData['ReferenceRangeSeries'] = "InRange";
-                            }
-
                         }, this);
 
-                        // for truncating out of range guideset data find last index of plotData starting from this.startDate
+                        // Mark the last index to truncate as j-1 (the point just before the user range starts),
+                        // so the first in-range data point is NOT included in the removed gap.
                         if (plotData.fullDate >= this.startDate) {
-                            if (!this.filterPoints[frag][plotData.MetricId]['filterPointsLastIndex']) {
-                                this.filterPoints[frag][plotData.MetricId]['filterPointsLastIndex'] = j;
+                            if (this.filterPoints[frag][plotData.MetricId]['filterPointsLastIndex'] === undefined) {
+                                this.filterPoints[frag][plotData.MetricId]['filterPointsLastIndex'] = j - 1;
                             }
                         }
                     }
@@ -392,6 +388,16 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
     renderPlots: function() {
         if (this.filterQCPoints) {
             this.truncateOutOfRangeQCPoints();
+            // Recompute showDataPoints based on post-truncation counts, since the gap between the
+            // reference guide set and the user's date range was removed and the remaining set may
+            // be well under the threshold.
+            var maxPointsPerSeries = 0;
+            for (var i = 0; i < this.precursors.length; i++) {
+                if (this.fragmentPlotData[this.precursors[i]]) {
+                    maxPointsPerSeries = Math.max(this.fragmentPlotData[this.precursors[i]].data.length, maxPointsPerSeries);
+                }
+            }
+            this.showDataPoints = maxPointsPerSeries <= LABKEY.targetedms.QCPlotHelperBase.maxPointsPerSeries;
         }
         // do not persist plot options in qc folder if changed after coming through experimental folder link
         if (!this.showExpRunRange) {
@@ -434,7 +440,7 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
         Ext4.Object.each(this.fragmentPlotData, function(label, fragmentData) {
             // traverse plotData backwards from firstIndex to lastIndex and
             // remove them from the array
-            if (this.filterQCPoints && this.filterPoints) {
+            if (this.filterQCPoints && this.filterPoints && this.filterPoints[label]) {
 
                 // when we're plotting two different metrics at the same time, then we
                 // have repeated dates (from oldest to newest for metric 1, and then oldest to newest for metric 2, all in the same array).