diff --git a/layout/reftests/z-index/reftest.list b/layout/reftests/z-index/reftest.list
index 1a7a7794d05e..a4a9b408ceef 100644
--- a/layout/reftests/z-index/reftest.list
+++ b/layout/reftests/z-index/reftest.list
@@ -1,6 +1,3 @@
-# Make overlay scrollbars never fade out
-default-preferences pref(layout.testing.overlay-scrollbars.always-visible,true)
-
 == 480053-1.html 480053-1-ref.html
 == z-index-1.html z-index-1-ref.html
 != stacking-context-yes.html stacking-context-no.html
diff --git a/layout/tools/reftest/b2g_start_script.js b/layout/tools/reftest/b2g_start_script.js
index bade89e5321f..416ceaf64da9 100644
--- a/layout/tools/reftest/b2g_start_script.js
+++ b/layout/tools/reftest/b2g_start_script.js
@@ -38,6 +38,10 @@ function setDefaultPrefs() {
     branch.setBoolPref("security.fileuri.strict_origin_policy", false);
     // Disable the thumbnailing service
     branch.setBoolPref("browser.pagethumbnails.capturing_disabled", true);
+    // Disable the fade out (over time) of overlay scrollbars, since we
+    // can't guarantee taking both reftest snapshots at the same point
+    // during the fade.
+    branch.setBoolPref("layout.testing.overlay-scrollbars.always-visible", true);
 }
 
 function setPermissions() {
diff --git a/layout/tools/reftest/bootstrap.js b/layout/tools/reftest/bootstrap.js
index 36ab76cc348d..d4b2ed70f0b2 100644
--- a/layout/tools/reftest/bootstrap.js
+++ b/layout/tools/reftest/bootstrap.js
@@ -38,6 +38,10 @@ function setDefaultPrefs() {
     branch.setIntPref("urlclassifier.updateinterval", 172800);
     // Disable high-quality downscaling, since it makes reftests more difficult.
     branch.setBoolPref("image.high_quality_downscaling.enabled", false);
+    // Disable the fade out (over time) of overlay scrollbars, since we
+    // can't guarantee taking both reftest snapshots at the same point
+    // during the fade.
+    branch.setBoolPref("layout.testing.overlay-scrollbars.always-visible", true);
 }
 
 var windowListener = {
diff --git a/layout/tools/reftest/reftest-cmdline.js b/layout/tools/reftest/reftest-cmdline.js
index 736d14b0a1de..1f6e5b320eb3 100644
--- a/layout/tools/reftest/reftest-cmdline.js
+++ b/layout/tools/reftest/reftest-cmdline.js
@@ -114,6 +114,10 @@ RefTestCmdLineHandler.prototype =
     // in our 800px window we don't zoom out by default to try to fit the
     // assumed 980px content.
     branch.setIntPref("browser.viewport.desktopWidth", 800);
+    // Disable the fade out (over time) of overlay scrollbars, since we
+    // can't guarantee taking both reftest snapshots at the same point
+    // during the fade.
+    branch.setBoolPref("layout.testing.overlay-scrollbars.always-visible", true);
 
     var wwatch = Components.classes["@mozilla.org/embedcomp/window-watcher;1"]
                            .getService(nsIWindowWatcher);