Three possible explanations:
1. Do you have an nForce board? The motherboard may have throttled the RAM back from 400Mhz (PC3200) to 333Mhz (PC2700). They do this to ensure stability when non-identical sticks are installed. You can normally over-ride this in the BIOS. I have an Asus A8N-Sli (an nForce 4 socket 939 board) and it switched to 333 when I installed a second pair of 2x512Mb sticks. Since all 4 were identical, I knew they should work fine together and cranked it back up to 400 with no problems at all.
2. You'll no longer be able to run dual-channel since you don't have matched pairs.
3. If you have an AMD CPU, the memory controller can only support 4 banks at 1T timing. So if you put more than 2 sticks in, it slows down to 2T (or do I mean the other way around? I can never remember)
Points 2 and 3 won't make much of a difference (a few percent maybe), but 1 can make a big difference. Luckily it's the noe you can do something about if you;re lucky. If your sticks are by the same manufacturer and have the same timings then you should be OK.