Something sounds wrong (duh). I doubt you'd notice any speed increase, as 512 is more than enough. But a slowdown? Are you using a matched set? Have you tried your new stick by itself, in the same slot as your original, to see if it behaves speedwise like your original? It could be something as simple as a defective stick. Can you borrow some known to good memory to try? Are you an Intel guy? Some AMD boards don't work right if all three slots are filled. That said have you checked any FAQ's at your mobo's site. Maybe a BIOS update is in order.
For optimum performance one large stick will always be the fastest (especially if you want to run CAS 2 timings). But this is more of a benchmark reading than the actual 'feel' of speed.