For a couple years my laptop's cygwin installation has been dramatically, inexplicably slow to start up the first time after rebooting. I mean, like, 5 to 10 minutes to start up. (You can imagine how much more this makes me love Windows Update for forcing a reboot every time they patch the latest buffer overrun that authorizes Solitaire to initiate a nuclear first strike against North Dakota.)
Well, today I found the culprit. A program I haven't used in quite a long time had left thousands of orphaned temp files in /tmp. Don't ask my why, but this was enough to obliterate the performance of cygwin across the board, and especially on startup. Maybe /tmp is memory-mapped? No idea. Anyway, I wish I'd known to keep my /tmp clean. Now you know.