Cross references DO update automatically, which is why I suggested them to begin with.
I'm not suggesting there's a problem with your hardware (I have a home-built system, too, and have been building my own for years), but you might be running something that has a conflict with ID. If I see a crash in ID more than once a year working with my own files (I get a lot of test files that crash, but that's why they get sent to me) I would say that was unusual.