I have identified and resolved.the issue. There is a bug with how Premeire Pro handles importing videos with variable frame rate.
Community Memeber Walter.Johnson found a work-around at the bottum of this post, which also has the identification and submission of the bug itself:
I had to convert the video with "constant framerate" selected in handbrake. I'm believe the ffmpeg CLI equivilant switch is "-cfr" but I have not tested to be sure.
I can now import videos with synced audio!
I have recorded several hours of footage using a program called XSplit (a screen recording tool).
The files are recorded in a FLV format and I then convert them to MP4 as premiere pro cant read then in FLV.
In a MP4 format I can import the files into Premiere Pro CC and the video looks perfect, but the audio is unsynced. It is also unsynced in non-linear way so it is not something that I can simply unlink and adjust to compensate as it would have to be done manually every minute.
If I import these same MP4s into other video editing programs they import perfectly fine and have no audio sync issues what-so-ever. I only experience this issue in Premeire Pro CC. I can even tested these videos in 6 different media players and they play perfecly fine.
If I convert the files to AVI using ffmpeg or ffmpeg assisted tools it will not import into Premiere Pro CC and gives a "unsupported format or damaged file" error. Once again, this avi can be played and edited in several other programs no problem.
Here are the details about one of these files:
VIdeo Codec: H.264/MPEG-4 AVC
Audio Codec: mp4a: MPEG-4 ACC LC
Audio: 44100hz 63 kb/s tot , stereo (2/0)
Anyone have any ideas on why the audio is becomming de-synced in Premiere Pro CC only?