I used to have that message (amd64, 2Gb of RAM). Today I'm having a
slight variation :

[    0.004000] Checking aperture...
[    0.004000] No AGP bridge found
[    0.004000] Node 0: aperture @ 28000000 size 32 MB
[    0.004000] Aperture pointing to e820 RAM. Ignoring.

I don't know what changed, in both cases I was booting
2.6.27-6.9-generic.

-- 
"Aperture beyond 4GB. Ignoring." message when booting
https://bugs.launchpad.net/bugs/271070
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