I keep having this same problem but it seems to happen with only one section of the video. The rest of the video will be alright.  What I have done is to go back and remake and re-edit the whole thing a second time and so far that has worked.  One thing to do is to make sure you go back and watch the whole thing after you do the editing to make sure it's all there still, then save it.  Another thing is that it seems to happen if I make any mistakes while editing.  Maybe I put the title in the wrong place by accident and have to take it out and put it back the right way.  Or, maybe when reviewing, I find a spot that needs to be taken out. 
When I make a video I am putting together several different "takes".  That's what it is supposed to be for.  I'm no computer expert so I hope I'm doing this right.  I have successfully made about 15 movies so far and have had this problem maybe 3 times.  So I can't see that it is a problem with the version of FRAPS that I'm using.  I think it has something to do with the way the "takes" are inserted or like I said, caused by something I do wrong when editing.  I just lost 6 hours of editing today because of this problem and I am HOT!!! to say the least. 
Also, it happens that today is the day my computer decides to do it's weekly backup (!!!) right when I am trying to save this video so I am betting that the timing has something to do with it too. When I say "editing" I mean the first time thru.  I do the titles and credits last and then watch it one last time thru to make sure everything is correct.  For some reason, the last time I watch it the whole thing is fuzzy but when it's finished saving it all clears up.  This time I had to make a change while watching the fuzzy run and didn't go back and make sure everything was still there.  ( Stupid me!)  So there's another thing to watch for.
I'm only shooting in the dark here but I think it's got something to do with the way you do it rather than the program itself.  For me it's looking at the instructions again and making sure I'm not making some stupid mistake.
I hope I have helped you out or made your brain click so maybe you can help me!!