I have been attempting to media manage a large documentary (roughly 3 hours of content split into 22 segments) and have had no end to problems with Media Mismanager, especially broadcast waves, though sometimes Quicktimes, too. Original complete project is 14TB, so it would take over 20 drives to redundantly archive everything, so Media Mismanager has to be used. There are other horror stories about Media Mismanager around the Internet.
I’ve tried a variety of solutions to the problem including making a copy of the original file and re-time stamping that (didn’t work).
The only solution I’ve come up with is rather long and convoluted, but seems to work consistently for broadcast wavs. I’m still testing it, but I promise to post full instructions once I’ve got it nailed down. It involves creating new media (wavs) using Final Cut’s export using Quicktime conversion and then re-timestamping the new media. There are a lot more steps (like 12), and I’m still fine-tuning it and trying to find a simpler method, so bear with me.
Mostly I just wanted to let you know that I feel your pain, and have been feeling that pain for several weeks now.