It's a registry cleaner and as such removes what it regards to be unnecessary files, the trouble is some of those files are important for other software to function. It's an old story. If it has a restore button all well and good, if not you'll have to uninstall McAfee, use the MCPR cleanup tool listed under Useful Links at the top of the page, reboot and then reinstall everything again from your online account.
Registry cleaners claim all kinds of benefits but they usually fail to tell you of their disadvantages and I can tell you from experience, their benefits are negligible.
If they have a support forum you might want to report this on there so they could maybe deal with it. There are just too many registry keys to consider. Their software should be geared to avoid all major software especially security software.
Their support may be able to offer you an answer.
Does anyone know which registry keys to tell FixIt to ignore?
Simple answer : no.
Registry cleaners mess things up, it's an acknowledged fact. We don't recommend their use, and neither do the Microsoft MVPs, who know about this sort of thing more tham most. If you have a problem after using Fix-It you need to contact Avanquest to sort it out - if you can find a way to do so. I've checked their site and here's their contact page, and it's not very helpful -
Their support is outsourced to SoftCity.com : you might try there.
You might also want to check user reviews of AvanQuest at WOT (here).