To: NSrailfan
Nevermind, under settings > processing I messed with some settings there.
Conversion:
Priority - Normal
Single-Thread Conversion
Resize:
Type - Super
Codecs:
Intel Media - Auto
Enable Enhanced Deinterlacing Method - CHECK
Enable Looping In SWF Files - NO CHECK
Enable Looping in DVD Files - CHECK
I'm not exactly sure what all these settings mean but for some reason this combination of settings worked.