With three cards the fans may have been running slightly faster to make up for the lack of airflow (just a wild guess). Try raising the gpu fan speeds a little and see if it helps with your 2 card setup.
And depending upon the exact version of your mobo with (2) cards your pci-e slots may run at X16 and with (3) cards they operate at X8.
And depending upon the exact version of your mobo with (2) cards your pci-e slots may run at X16 and with (3) cards they operate at X8.
