are pugged in fully???
In one configuration you will be running Dual Channel [512 in each channel] and the other 1 GB in one channel and none in the other. Either way Device mgr et al will report 1 GB. I'm sure that you know this, so have little choice but to think that soemhow the one stick has died.
Ant chance that the memory timing settings in the BIOS are causing a problem??
To run in Dual Channel mode the sticks should be using the same type on memory chips.
I recently replaced my motherboard and processor. I have 2 sticks of 512 mb pc3200 ddr400 ram installed. For some reason my computer is only recognizing one of them. My old motherboard and cpu recognized both of them. I have 4 ram slots [2 channel A (slots 1 & 3) and 2 channel B(slots 2 & 4)] and you have to have one installed in each channel. So I tried installing in every possible combination and it still only recognizes one of the memory sticks. WHY? I'm losing my mind working with this thing.

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic