I have been going through the same thing. I had also considered the MSI and Asus boards, but like you I kept reading about various problems with each.
To be honest with you, it seems like ALL of the A64 boards have issues. Some more serious than others. Initially I was just reading reviews of the boards on various sites, and I didn't see very many problems. However, when I started scanning user reviews and forum posts, the problems and complaints started to appear in vast numbers. The boards that appear to have the least amount of problems right now (from what I've read) are the Soltek SL-K8AN2E-GR, the ASRock K8S8X, and the DFI LANParty UT board, although the DFI hasn't really been out long enough to hear of many problems but it appears to be a pretty solid bet (as well as hands-down the best overclocking A64 board you can get).
It's weird because some people will claim to have no issues with a particular board or setup, while for others a similar setup will prove to be a nightmare. I think part of the problem is that A64 boards seem to be picky about memory, but I'm starting to read about people having SATA/IDE issues as well. The good news is that some of this is fixed in BIOS releases as time goes on, but it's best to do some research before you buy instead of blindly picking a product because you read posts from a couple of people that liked it.