You were better off with Windows 2000 than ME it is a much better written program and more stable.
Though you may have compatibility problems with some games and other programs in 2000 most of these can be solved by downloading updates like service packs 1 & 2 from Microsoft.
From what you're saying I'm assuming you still have Win2000 on your system as a dual boot. If you want a 9x version of windows on your system I suggest Win98se it has less problems than ME and is compatible with just about everything.
Also make sure you have the correct sound card drivers installed.