Welcome to our community, Brian!
Yes, this issue was probably the single most reported issue
when Captivate 2 first came out. The disappearing menus!
If you have been paying attention, you will have noticed that
this happens after you interact with any Flash object in your
project. Certainly restarting Captivate corrects the issue, but
that's a bit on the drastic side. Here is how you may stop the
flashing.
After you interact with a Flash Animation object, click
anything over in your Library panel. The goal is to simply place
focus there. Once you do this, the menus should stabilize. That is,
until you interact with another Flash Animation.
Cheers... Rick