Hi,
I have received no answer to my former question
(see http://marc.theaimsgroup.com/?l=linux-kernel&m=110827143716215&w=2).
I've spent some more time on that problem and have more or less confirmed
it's because of buggy bios. However, the linux kernel doesn't handle properly
such case. I've tested 2.4.30-pre1 kernel and latest 2.6.11-rc4 kernel.
The conclusion is, that once the machine has physically installed 4x1GB
DDR400 DIMM's (bios detects only 3556 or less memory as some buffers
are allocated by the Intel 875P chipset and AGP card), the linux 2.6.11*
runs up-to 18x slower than when only 2x1GB + 2x 512MB DDR memory is installed.
Can you enable profiling and then post the profile info for various cases
- slow and fast? Check out Documentation/basic_profiling.txt in the kernel
source for understanding how to do this. This might help narrow down the issue.