Ahh Rosetta, makes more sense.  Credit for workunits is not a constant.  It depends how many models are completed and returned with the result.  Their credits are based more on the contribution to the science and they handle credits different than other projects.  They have a pretty lengthy description of this at the Rosetta site.   SOme workunits are simpler than others and more models get completed.  Id look inside your results to see how many models were completed. 

Could there be something on the machine sucking up cycles?

I think it has more to do with the hyperthreading than the project. Even though it is taking the same amount of CPU time the AMD is using that time more efficiently (fewer cycles per instruction). If the AMD number is similar to the speed of the intel processor then they should be producing similar amounts of credit per day.