diff --git a/src/checkable_continuous_flyout.js b/src/checkable_continuous_flyout.js
index fb076aabc0..9d75cd53be 100644
--- a/src/checkable_continuous_flyout.js
+++ b/src/checkable_continuous_flyout.js
@@ -104,6 +104,26 @@ export class CheckableContinuousFlyout extends ContinuousFlyout {
     this.checkboxes_.clear();
   }
 
+  layout_(contents, gaps) {
+    super.layout_(contents, gaps);
+    // We want large gaps between categories (see GAP_Y), but don't want those
+    // counted as part of the category for purposes of scrolling to show the
+    // category, so we reset/adjust the label gaps used for the scroll position
+    // calculation here.
+    this.labelGaps.fill(
+      this.getWorkspace().getRenderer().getConstants().GRID_UNIT
+    );
+  }
+
+  calculateBottomPadding(contentMetrics, viewMetrics) {
+    // Since we're messing with the alignment by munging the label gaps, we also
+    // need to adjust the bottom padding.
+    return (
+      super.calculateBottomPadding(contentMetrics, viewMetrics) -
+      this.getWorkspace().getRenderer().getConstants().GRID_UNIT * 4
+    );
+  }
+
   addBlockListeners_(root, block, rect) {
     if (block.checkboxInFlyout) {
       const coordinates = block.getRelativeToSurfaceXY();