I've noticed that for the last couple of builds IntelliJ will have noticeable pauses. Today I copied a file from one instance of intellij to another and the application locked up for 45 seconds. A co-worker who downloaded IntelliJ today is having the same problem.
Both of us are using the Ultimate Edition, my build is 1116.4
Both on Windows 7 Pro
I allocate 4G to my instance