Have that message on my laptop too, as well as problems, though booting is 
fine, waking up from suspend / hibernate causes problems.
Aperture beyond 4GB. Ignoring
Your BIOS doesn't leave a aperture memory hole.
Please enable the IOMMU option in the BIOS setup.
This costs you 64MB of RAM

Sympton is freeze a second or so after waking up (hibernate / suspend).
Laptop has had a fresh 8.10 install after purchase in Nov 2008.

System HP Compaq 6715b AMD64 Turion TL62 2,1GHz, 4GB
VGA compatible controller: ATI Technologies Inc RS690M [Radeon X1200 Series] 
Wireless: BCM4312 802.11a/b/g (rev 02)
Ethernet controller: Broadcom Corporation NetLink BCM5787M Gigabit Ethernet PCI 
Express (rev 02) 

https://wiki.ubuntu.com/LaptopTestingTeam/HPCompaq6715b

I believe that the freeze symptom is related to that message, because I found 
several discussions which point problems/solutions involving IOMMU / AMD64. 
(mem=4G ,...)
http://lkml.org/lkml/2008/5/25/228
http://thread.gmane.org/gmane.linux.swsusp.general/7777

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