Alright so I used GSpot to sniff one of the affected source files and it said " 0x0055 MPEG-1 Layer 3".
Google brought up this site
0x0055 - MPEG-1 Layer 3 (MP3) - Codec Library
which then links to saying this:
"MPEG Layer 3 (Elecard)
This uses LAME 3.88 beta
MPEG Layer III encoding engine.
More Information located at
www.mp3dev.org - mp3devĀ*.
"
Which didn't make it work. I think I even already had LAME. I have almost 500 codecs installed.
One detail I didn't mention is that even when I try to drop the source file in anywhere it immediately shows the video but not the audio. Knee-Jerk. I encounter this sort of thing when trying to load things all the time but this time it was working before with the now non-working files.