Mac Pro CPU temperature discrepancy
I upgraded my 4,1 Mac Pro to a pair of X5690s and am seeing exactly the same Tdiode temperatures as you - CPU A around 61°C and CPU B around 46°C at idle.

It seems to be normal owing to the inline airflow and discrepancies in heatsink size. As others have said, as long as the Tcase max temp is not exceeded on either CPU, I think we're fine and can rest safe in the knowledge that it's not due to bad/inconsistent thermal paste application.