I have some Fraps footage which has been converted using AviDemux 2.5 into what it calls the 'MP4' container format using the 'MPEG4-AVC' codec (which as I understand it is another name for H.264). This is the only combination I've found so far that seems to work decently between AviDemux and Premiere Pro. The recording is 640x502 square pixels at 30.0 fps. I have imported this file into Premiere Pro CS 5.5.0 on a MacBook running OS X 10.6.8. The sequence is set to 640x480 square pixels at 30.0 fps (so I've downscaled the footage vertically to 95.6% via the built-in Motion effect as this looks better than letterbox bars).
Some of the scenes in the footage are really dark, so I'm applying a Shadow/Highlight effect to enhance them, and adding an overlay image to indicate that those scenes have been enhanced for the viewer's pleasure. The transitions between dark and bright scenes in the source video are often instant, so the effect and overlay both need to be turned on or off with single frame precision. I've used the razor tool to separate the dark scenes from the bright ones, added the Shadow/Highlight effect to the dark clips, and placed the overlay on a separate video track above the dark clips. I chose not to use keyframes for this since it allows me to snap overlay clips and dark clips together easily. It also avoids cluttering the sequence with effects that aren't in use 95% of the time.
Most of the time I can edit with perfect frame accuracy just fine, but suddenly some of the cuts I've already made will begin to match a different frame within the source footage (at least if I go by the program monitor), though never more than two frames from the original position from what I've seen. Since I was rather confused the first time this happened, I went back and fixed all the edits by dragging the edges of source video clips and overlay clips to match the source video. This worked fine, until suddenly it happened again, and lo and behold, when I tried to fix that I was actually undoing all the edits I had just made.
Since then this has happened a few more times, and I've come to some conclusions. The video clip boxes don't seem to be moving within the timeline, and neither do the overlay clips (which are always in sync with the Shadow/Highlight effect, but not always with the source footage). The audio timing seems unaffected (ie. as far as I can tell it does not seem to move within the timeline when the video content does). Strangely enough, this frame shift only seems to happen for some of my cuts, and the mismatch is in some cases by one frame and in others by two frames, which I find rather odd since as far as I can tell the source and sequence framerates match perfectly. All this seems to imply there is a problem with the video codec's frame lookup and/or synchronization, or possibly a video timing glitch in Premiere Pro, but I don't know how to confirm or disprove either theory.
Does anyone have any suggestions or ideas that might help fix or at least shed some light on this issue?