I replied to one of your replies elsewhere, but here it is again. I had a similar issue where only some commercials were getting removed. I found that I also needed to go to Settings > General Settings > System Settings and change the Minimum Commercial Duration from the default of 20 to something smaller (I used 4 seconds). This is because some Hulu commercials are less than 20 seconds long, so they get left in by default. This works well if you only use MCEBuddy for this kind of commercial removal. However, if you are doing commercial detection using Comskip or ShowAnalyzer, this might cause the results to deteriorate. It would be nice if this setting could be specific to the Conversion Profile.