This is probably a silly question, but I am curious what others have to say on this....
I have been running 2x1gb ddr 800 sticks on my pc for a while now. Well the same sticks were on sale so I got another 2x1gb for the heck of it. I realize my version of windows can only see 3gb, but will that bog my system down since only 2 are being run in dual channel mode? Can to much on-board memory in xp 32 actually slow your system a bit??
If you are losing dual channel for whatever reason, yes it will be slower. I don't know why you would though.
Otherwise, no it won't slow you down in any meaningful way. It may run at the 2t command rate instead of 1t, but since you are asking this question, you probably won't care or notice.
It won't bog you down, but it might not be the best performance upgrade for your system. For example, adding a second hard drive (not RAID) would give you a lot more bang for the buck if you're only running one, effectively doubling your data I/O.
My system has 2x2GB and XP32 and it's not bogged down at all. I see 3.25 GB. Other people (with different video cards) see 3.5. You should be fine.
Are you sure that only 2 of the 4 sticks will run in dual-channel mode? Did you read that in the motherboard's manual? I would expect it to work with 4 sticks. Either way, it won't hurt performance noticeably, and when things get really tough and the additional memory is actually used you'll see a huge performance gain. http://en.wikipedia.org/wiki/Dual-channel_architecture
You should be able to run all four sticks in DC mode. You might drop to 2t command rate, or the ram might drop down in frequency/have looser timings, but I'm not sure if the system will be slower overall. If you use programs that require lots of ram, they will probably run faster overall due to needing to use the swap file less. However, you your ram uses never exceeded 2GBs, you could find things running a bit slower. (2t command rate @ 5-5-5-15 instead of 1t command rate at 4-4-4-12)