Video and Audio out of Sync - Only on my Bold 9900 and not on my computer

I have been converting .avi files to .m4v files using handbrake and putting them on my Bold 9900 simply through the click and drag method as if my bold (and it's media card) was an external hard drive. Most of my files that I have done this with are giving me no problems.
Some of the files play the audio about 2 seconds before the video, right from the start of the video and scrolling (ff or rewind) does nothing to change the sync. Hard resets do nothing and the very same video files play perfectly fine on my computer in QuickTime and in VLC player. It only screws up on my Bold 9900.
I have also tried deleting the files and reconverting them using the same file name, and again using a different file name. I have also tried altering the bitrate of the video of the file and that doesn't change anything either.
I need help!
Any advice would be greatly appreciated.