I have the same 2 cards and having the same issue. It is almost like one card is working and the other is not. I downloaded the newsest driver, checked my SLI bridge and both cards individually, and they work fine independently. However, dont think SLI drivers are working very well. The cards do not share the load evenly from what I have gathered.
In the driver highlights on Nvidia's driver page from the link above, it says that the new driver enables sli on the 990 fx Chipset. However, I did this and it shows both cards in SLI under the nvidia control panel.
The GTX 560 TI SC closest to the CPU is so hot and the other card below in the second PCIE X16 slot is so cool.
THere has to be a problem. Let me know if you figured this issue out.
Your score really isn't much lower than average, I don't think there's really a problem. I had a similar score with a similar system. The funny part was when I ran the extreme test (EVGA cards can be registered for a full key to 3D mark 11) I ended up in the top 10%.
You can go through and update drivers and your BIOS, overclocking would also bring your scores up. Unless your score ends you up a thousand points below average there probably isn't much to worry about.