Wow, that is weird. You could try rendering out a png sequence, import back in and see how it looks? If it's fine then try exporting that out as your final render. If it's still dodgy as a png sequence, we'll have to think of something else, if the png's are fine but you can't then export a QT without issues, then you might have to dump it into Premiere for a final export. It's not solving the underlining issue but if you're struggling for time then it'll get you through for now.
In fact, install the latest version of QT in case its that
Purge you image cache and empty the disk cache. This could be caused by the codec of your source footage. This could also be caused by having render multiple frames simultaneously turned on if you have a pre CC2015 version of AE. The default Lossless format on windows machines is different than the lossless format on a Mac (Animation Codec Quicktime) so something could be fouled up there if you have 3rd party codec packs installed or some screen capture software that brings in it's own formats. I'd either try rendering to Quicktime Animation Codec or Quicktime JPEG or to an image sequence or if you want to just render directly for delivery use the Adobe Media Encoder and choose one of the h.264 presets that matches your intended audience.
BTW, AE and AME should both be up to date.
Sorry I have been out and haven't been able to get back to this until now. Thanks to both of you for your response! I am not currently under a deadline for this now. The QT render was good enough. I only had to remove about 3 frames. Since I am relatively new to AE I'm not sure what all the recommendations are, but I will try them and get back to this thread in the next couple of days. Thanks again!
My apologies. I should have known better than to render to an external drive. I rendered to an internal drive and the problem went away. Totally reproducible. Thanks for your help!
Rick, I know you from about 20+ years ago in Issaquah. Good to see you again. I sent you a friend request.
Take care all.