I’ve used Fraps in the past without any problem, including fairly recently capturing some Google Earth footage. First, make sure that you have the latest version of their 64bit codec installed. If that’s not the problem, you could always transcode Fraps into a lossless codec that is Vegas friendly such as Lagarith, Magic YUV or UT Video. You can use the freeware Virtualdub to easily do this. Alternatively, you could try a different capture package such as Mirilli’s Action (I believe they have a 30 day trial period). I found that with my system, at least, there were fewer dropped frames with Action as opposed to Fraps and a lot more options for Desktop capture. Or lastly, you could try different editing software. Lots of options.
wwaag
Just a thought. Have you rendered other projects involving different source material? If not, you might give that a try. Although Fraps seems to be the likely culprit, it may be that the problem has nothing to do with Fraps at all. Worth a shot to try using same render settings but with different source material to see if you still have the problem or it disappears.