There are two main reasons why I would indeed believe that the MacOS Intel version is slightly faster than the Windows one:
1. You usually have something more running in the background on Windows than on MacOS (virus scanner, application-level firewall etc) which "steals" some time from BOINC.
2. As the Intel Macs all have the same CPU (or at least the same CPU features) we don't need to detect CPU features and switch codes optimized for different CPUs there, which is what we do in the Windows App. However I doubt that this alone is responsible for a speed difference as large as you observed.
BM
