Don't use uncompressed. Not only does particleIllusion have problems with it under some unknown conditions for some people (like you've seen), but it's a waste of HD space.
Use a lossless codec like huffyuv or Lagarith. They result in perfect ("lossless") image quality (identical to uncompressed) but result in much smaller file sizes, use less bandwidth when transferring (during playback for instance), and most importantly: always work in particleIllusion.
And for those of you who say "I don't want to use *any* compression on my video because I want the best quality" -- "lossless" compression *is* the best quality. Have you ever zipped a data file? That's lossless compression -- the file after zipping and unzipping is exactly the same as the original file.
Alan.
http://www.wondertouch.com