Thanks for the suggestions. Unfortunately, no luck. Some new info: this only happens with (some) MKV files. All MPG and MP4 work perfectly. I have combos of DVD (480) and HD (1080) in all 3 formats, and only some of the MKVs (both types) do this. To further complicate matters, I have tried these movies on 3 different computers in MC 25 and the only problem I have is with my new i5 setup.
Another note: on the i5 computer I can use VLC and every problematic MKV plays perfectly. I have checked MC settings on these computers and they are all the same. For example, Sox is unchecked on all (and I tried checking it on i5), Red October is selected (and I tried custom), VideoClock is the same, etc.
I have a suspicion that handbrake is the culprit. I don't have a log of which files I rendered with it, but it's the only thing I can think of. But why on only 1 computer??? Also I read something about VBR vs CBR video causing the audio to get out of sync. I guess if audio was expecting CBR but file is actually VBR? But again, why on only 1 computer???