that's odd. what lossless codec are you using as the intermediate? did you check that the frames are there in the new master file in vdub? worst comes to worst you may need to duplicate the last minute or so of frames (i think you can just copy/paste) in vdub before exporting, then trim off any excess in yua ...
SDA Forum
for posterity, the solution was to export uncompressed nmf from vdub, then feed that into yua. the problem seems to be related to the fraps codec recording delta frames with zero differences from the previous frame rather than insertions to achieve constant 60 fps. not sure why uncompressed nmf would solve the problem and huffyuv (in which every frame is also a keyframe) not, but hey i'm not complaining. also, ffmpeg's fraps decoder seems to have the same problem.