So... I'm still having trouble with this. Thanks to those who've replied so far.
I'm going to try calling tech support about this in the morning. Any of you guys think that would be futile?
Right now my basic thing to get around this is
1) Save a copy of the project
2) Open both the copy and the working project
3) Add new section of improv and do my set to measure/beat thing
4) copy stuff from the project copy into the working version to replace all the clips that get truncated.
It's pretty darn frustrating!