some good advice I should have followed (because I knew full well!): never use any Windows-based BIOS update utilities.
Anyway! having since realized I could just use a USB flash drive to install the BIOS from through "EZFlash", I flashed the new 0701 BIOS onto my brand new board. After checking that it would still boot my old setup, I threw in the HD3650, installed the fglrx 8.3 packages I built last week, edited /etc/ati/authatieventsd.sh to point to /var/run/xauth, and finally found absolutely no difference to the lockups on logout and when starting an additional Xserver.
zappbrannigan: I read the thread you linked but I don't see any info on what you did to your mtrr... Here's the output of cat /proc/mtrr on my system (but with my 8600gt installed, I don't know if that matters):
I'm pretty sure I don't have any memory remap options in my BIOS, if there's something I can do with the mtrr please let me know.
reg00: base=0x00000000 ( 0MB), size=2048MB: write-back, count=1
reg01: base=0x80000000 (2048MB), size=1024MB: write-back, count=1
reg02: base=0xc0000000 (3072MB), size= 256MB: write-back, count=1