Ok, so from you said, it sounds like it's the java app causing the problem.. So, maybe try uninstalling that app and see if it helps any.. If so, then you know what the problem is..
I know alot of other people were having problems with Java on the 64-bit version as well. Many had to uninstall Java OR reinstall Windows..
Why is there no use of trying a system restore? If the problem just started happening than a system restore may fix it..
Or at the very least it will point us in the right direction..