--- main.cpp.orig	2013-11-05 10:26:42.294071874 -0600
+++ main.cpp	2013-11-07 23:38:31.841413311 -0600
@@ -636,7 +636,8 @@
         if (useCutlist)
         {
             LOG(VB_GENERAL, LOG_INFO, "Honoring the cutlist while transcoding");
-            pginfo->QueryCutList(deleteMap);
+            if (deleteMap.size() == 0)
+                pginfo->QueryCutList(deleteMap);
         }
         if (jobID >= 0)
         {