I believe it may be your motherboard. I was working on an older Compaq P4A machine, and the BIOS kept telling me it only had 128MB of memory, despite the stick being a 256MB stick. I put it in a different machine and it came up as 256MB. I couldn't blame the CPU, as it had no memory controller on it, so I got a new motherboard for it and all was well.
The difficult part of it is that you're running an A64 with an ondie memory controller. It's hard to be sure whether it's the memory controller or the motherboard that went bad. Any way that you can get a s754 mobo or A64 to borrow and test this out with?