Well, this was ripped from a DVD using Handbrake and transcoded to .mp4 and H.264 codec so I wasn’t anticipating this sort of problem. There were 4 DVDs – two about an hour long and two about 90 minutes. It could be coincidence but, the hour long presentations are synced just fine. All the files aren’t particularly big in any case.
I do have MPEG Streamclip so, I may just try that for the hell of it. Thanks for the suggestions!