I can tell you that I don't currently have PocketPuTTY installed (I should get it though) and I have the same annoying bug. So that's not it either.

FWIW- I think I'm seeing a trend that this occurs when multiple Alerts are coming in at the same time (ie. a small SMS flood).

I recall having this issue on one my Treos way back and I believe a firmware fixed it. I could be wrong though...

I think I'm just going to disable vibrate for now.