thewumpus, I had a similar problem that popped up a few weeks back. Often times when clicking the interface (and almost always when firing off a fish, it seemed

) I would get the most horrible sounding screeching, hissing, staticy (is that even a word???) sounds that it would make me jump half out of my chair. Sometimes it would continue for several minutes, stop, and then come back later on. I tried reinstalling SH4 and 1.3 and the Xi-Fi drivers and it didn't work. Games like BF2 and STALKER had no issues. My PC was due for a fresh XP image so that's what I ended doing and I've had no issues since. I'm afraid to try and sound mods now which sucks because I really like some of them.
Good luck with the problem. Please post if you find a definitive solution.