From what I've heard, that's a problem that affects video recording in FRAPs too. Basically it happens if the drive you're recording the file to is the same drive as the game/program you're recording from (say, Trainz) is also installed on - because the hard drive is having to read and write to the same drive at once, it's doing more work - hence the skipped frames. The only way to avoid this from what I understand is if you have a second hard drive installed on your system, to record the video to that and it should fix the problem.