It occasionally helps because some mods like to store things there, and will screw up if you leave them and try to reinstall.
One more thing to try: Clean out all Java versions, reboot your computer, and reinstall the newest 64-bit version of Java 7 (u7, I think). If you don't reboot between installs, your system sometimes fails to empty the garbage can, so to speak, and the multiple versions of Java get confusificated.
Then check your system path variable to make sure Java is in there correctly (i.e. it points to the right folder).