Ac3 to Anything Audio Boost?

I have a heap of DVD's that I need to (Ideally) convert to QuickTime (ProRes) but using Episode or MPEG Stream Clip I have noticed the audio is raised and sometime distorted compared to demuxing/extracting the AC3. Has anyone else experienced this? If there was another way around demuxing all the DVD's I have and rejoining them that would be preferable. I have tried some software I have on a PC, Adobe Media encoder and Procoder both give me great results with no audio level adjustments but I can't create the ProRes files I want to :(