Interestingly, I ran NWChem 6.0 on 64 and 16 cores (each with 1 GByte of memory per core, set as memory 1000 mb in the input) and both sets of calculations gave exactly the same results. Hence, I have no clue why you see the differences. The only way to track this further is for you to reproduce the results for NWChem 6.0 for 40 and 48 processors using the same input deck for both.