Some of the problems I have run into have been my own doing.

Like with Java, I know I should have shut down everything first, or at the least my browsers.

AntiVirus. I have had AVG, F-Prot, & SAV all installed & running - at the same time, though not necessarily simultaneously. (SAV not installed till today).

I have a tendency to run programs, might you say, in a (possibly) less then desired fashion. Perhaps without actually installing it, or whatever. In general that is no problem. It appears to be more of a problem in Vista.