Mouse freezes, then Windows plays standard sound

My mouse occasionally goes unresponsive for a few seconds (keys still work properly, so it's not a general game freeze), then resumes with Windows playing its standard "something just happened" sound, with no clue whatsoever what happened.

This has started only recently, though I can't tell for sure what change got it started; some gut feeling tells me it might be related to the LWJGL version bump. (It might even be something entirely unrelated to Minecraft, but so far I haven't encountered the glitch anywhere outside the game.)

Any ideas how to narrow down the root cause would be appreciated.