So.. that's a little odd. After I renamed that file and it didn't work, I rebooted the machine to see if that would make a difference and it's worked ever since. I left off reporting back so I could test it a little more thoroughly to make sure.
I didn't know the WACUP installer did the 5.666 as well, that's handy.. but previously I had tried just that one (after uninstalling the Winamp 5.8 dealie (i was curious)) and it wouldn't launch at all then either, which is when I did the 5.666 install and then WACUP over the top of that. The WACUP installer was downloaded from here, and the 5.666 was downloaded from the old winamp site way back when. When it was stuck in the background I didn't notice it using processor time, certainly not much if any.
Anyway, seems it's fine now, I'll report back if it goes wrong again.