You should be able to convert them to standard x264 using ffmpeg...
I think this command should do the job...
ffmpeg -i "input.mp4" -vcodec libx264 -acodec copy "output.mp4"
EDIT: If that doesn't work, try this...
ffmpeg -i "input.mp4" -vcodec libx264 -pix_fmt yuv420p -acodec copy "output.mp4"
According to the ffmpeg H.264 docs...
You may need to use -pix_fmt yuv420p for your output to work in QuickTime and most other players. These players only supports the YUV planar color space with 4:2:0 chroma subsampling for H.264 video. Otherwise, depending on your source, ffmpeg may output to a pixel format that may be incompatible with these players.
GroovyMAME support forum on BYOAC