I've posted a couple times before about my sound desync/skipping issue. It seems to be the same problem a bunch of other people have been having. I haven't been able to run any version of Nestopia (including 1.36) on this computer since I upgraded to Win7, though I can run it fine on a Win7 laptop. There are no other NES emulators that I find acceptable, so I'm pretty much stuck.
Today I happened to fire up the emulator just to take some screenshots of games, and I did some troubleshooting. What I noticed is that when I load a game, CPU usage on my machine (single-core 1.8ghz Athlon 64) starts out around 32-38% but climbs in fits and starts, maxing out the CPU within a minute or so. The sound problem only happens while CPU usage is climbing. It sounds fine when usage plateaus for a few seconds. Sometimes usage will drop back to the 30s and the emulator sounds perfect, until CPU usage begins to climb again.
Has anyone else noticed this behavior? Could this be a clue? I've tried messing with every option I could find, including obvious things like process priority, timing, disabling sound, etc. No other CPU-heavy processes are running.