I am using IntelliJ IDEA 12.1.6 on (64-bit) Windows 7 Enterprise (I've also seen this same problem with IDEA 11, though not as often). I am running it under Java 7 (1.7.45).
When I run a program in the IDE, under the debugger, everything is fine until I hit a breakpoint (these are plain old on-a-specific-line breakpoints, not method breakpoints or exception breakpoints). Once the breakpoint is hit, virtually all the time (though not always) my entire machine slows to a near halt. All keyboard operations (not just in IDEA) slow way down (they eventually do get processed so the events are buffered, not lost). Same for window operations (drag, minimize, raise, lower). Once the program resumes from the breakpoint everything goes completely back to normal until the next time a breakpoint is hit.
This is obviously really annoying as it makes debugging essentially impossible.
I've had Task Manager up and don't see anything strange. The CPU is not pegged, memory isn't maxed out, etc. My hard drive light isn't on.
Any ideas on what's going on and (more importantly) how to fix it?