Had a reply from Gigabyte - yes, it *is* a BIOS bug, and the BIOS upgrade fixes 
it. The kernel bug was rejected as invalid (because it's a BIOS problem, not a 
kernel problem).
I'll give full details below, because this wasn't quite straightfoward to fix, 
and hopefully it will help someone else.

1)Get the latest BIOS update from gigabyte. I used this one
successfully:  motherboard_bios_ga-p35c-ds3r_f4g_beta.exe

2)Extract the BIOS with wine (0.9.41 works fine). Gigabyte don't provide
the md5sum, so, for info:  6f283d38e272ea433b4478f39a6cdb03
P35CDS3R.F4g

3)Copy the BIOS onto a floppy. [The manual claims that a USB key is also
supported: the Q-flash utility loads the new image fine, but fails at
the last step with "BIOS ID CHECK ERROR". You have to use a real old-
fashioned diskette.]

4)Flash BIOS, Load optimized defaults. Enjoy.

5)Once updated, free -m reports 8002 MB free (presumably, the rest is
used by the kernel). The MTRRs are now:

$ cat /proc/mtrr
reg00: base=0x00000000 (   0MB), size=4096MB: write-back, count=1
reg01: base=0xe0000000 (3584MB), size= 512MB: uncachable, count=1
reg02: base=0x100000000 (4096MB), size=4096MB: write-back, count=1
reg03: base=0x200000000 (8192MB), size= 512MB: write-back, count=1
reg04: base=0xdff00000 (3583MB), size=   1MB: write-through, count=1

And the performance is about 50% better than the best it was before :-)


I'm sure Gigabyte have shipped lots of boards with the original broken BIOS - 
is there any way to make the kernel print a warning? It would be nice if the 
next Ubuntu user who hits this bug can find the fix more easily! 

Thanks once again for your help - Richard

-- 
kernel performance is *very* slow with 8GB RAM on AMD64. 6GB is fine. kernel 
2.6.22-8 x86_64
https://bugs.launchpad.net/bugs/129172
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