It shouldnt have any problems reading two sticks of different sizes.
[strike]Tho if your running dual channel with those two sticks, you will probably only have 2Gig available anyways. [/strike]
Edit: when thinking about it, you should have all 3 gig available in Dual channel configuration, the motherboard should map the 1 gig stick, and 1Gig on the new stick for Dual channel operation, the remaining 1 Gig will be mapped for single channel operation. Or something like that, cant entirely remember it.