I thought it was worth adding this, even though I'm running Gentoo, it seems to be exactly the same issue:
I recently upgraded to ext4 as well, I ran a game in Wine and the system hardlocked (nothing special there with the fglrx drivers). After rebooting all my Wine registry files were 0 bytes, as were many of my Gnome configuration files. Absoloute nightmare. fsck on boot said that it had removed 760+ orphaned inodes.
/dev/root on / type ext4 (rw,noatime,barrier=1,data=ordered)