Thanks for the response Jerry! I think you may be right about things getting corrupted, I have been playing ping pong with my files over a few hard drives and maybe something got messed up.
After some transcoding tests I found that the custom presets I made for this project will not work with any other file but the files for this project will work with Compressor’s MPEG2 presets, so in the meanwhile as a quick fix I will just remake the presets and not the files.
Thanks again!