The code the diffeent BOINC project use might be suited better for certain CPU architectures than for others. E.g. it seems that E@H perfoms better on AMD CPUs than on Intel ones (with comparable clock rates and overall performance) while SETI may be the other way round. The WUs of E@H are constant (well, small difference may occur). There are some threads here discussing the runtimes of E@H WUs on different (types of) machines, one title I remember is "Curious run times".
BM

How is WU size matched to CPU?
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> In short, the WUs are not generated specially for any particular machine.
> Some projects have more than one application (Protein Predictor has MFold and
> Charmm, and Pirates has a dozen or so). Some of these different applications
> may require more memory or more run time than is available on a particular
> machine and that machine will not get WUs of that type sent.
FWIW, all the E@H workunits have the same size and memory restrictions and should take the same number of cycles to run. However this is strictly speaking not true, since depending upon what is in the data, the search algorithm may have to do a different amount of work, and the memory and file usage may be quite different. But when the scheduler sends out work, the disk/memory/cpu requirements for all the WU are the same.
Bruce