This does sound like a Vista-specific issue, but I think the problem is either with or caused by a third party tool (either PNGOut, the java thing, or Steam). I've noticed there's a new version of PNGOut available; I'll update it for the next build, and hopefully that will resolve it.
I might mention... if you upgrade to Windows 7 or 8 you also get automatic AAC encoding when you import audio. Might be worth considering :P