I'm not sure if it's related, but I'm noticing some strange behaviour of java6 at work:
Sometimes the whole OS (still running Win2000 here) almost freezes completely! When that happens (sometimes 5 times a day, sometimes 2 times a week), trying to kill all java processes solves the problem (that is, if the OS isn't frozen too much).
The problem seems to be triggered by running java6 and a java 1.4.2 version at the same time, as axing Lotus Notes' JRE (1.4.2) and replacing it with a java6 JRE seems to make the problem almost go away (making all applications use the same java6). Weird but true
. There's still the occasional short, system-wide pauses though...
Cas, does Ultratron still have the same problem if you run Eclipse with the same JRE version as Ultratron?