Running 3 x GTX 260 should not be an issue unless one of them isn't working right. The fact that their clock speeds are different should not matter either, as they will all be forced to run at the same speed as the slowest card.
Do you have anything OverClocked? Or is the third card overclocked to match the other two? Also make sure you download and install the latest nVidia graphic drivers for your OS as well.