I think we all know that it's not advisable to run wine as Root, just for caution and because of possible malware. But even without viruses or the like, it seems to cause problems in itself: I used to run an audio program as Root under Wine. I didn't notice the connection immediately, but my hda started to be unbootable on every reboot. I would fix this by "dd if=backupfile of=/dev/hda bs=512 count=1"; the beginning of the drive would be screwed up. And it appears that this happens every time Wine has run as Root, and never when it hasn't. Nothing else is corrupted, but for some reason, it loses the partition table.