make sure in your bios the memory settings are set to Manual (ie you specify them), then i would play around with some of the memory settings.
The problem you have is latencys, your 2 x 512MB will run @ PC3200 2.5-3-3-6 or something like that, where as your 2x1GB will run @ PC3200 3-4-4-4-8 (alot slower), your motherboard is probably setup to run the memory @ the original memories speed, therefore trying to run your 2 x 1GB @ 2.5-3-3-6 (way to fast for 2x1GB).
try setting all your memory to 3-4-4-4-8 2T