If it's on a hyperthreaded machine, this is to be expected, to compensate, increase the number of threads to 5 for a single core, 2 thread chip, or 10 for a dual core 4 thread chip.
If it's on a multithreaded system with sync'd clockrates for each core, then wPrime didn't sync it's threads properly, press ~, type initthread <enter>, then type gui <enter> and try again.
In fact, this might be an explanation for the difference in speed between different versions. Will post some results shortly.
Standard Sync: http://wprime.net/score.cgi?id=14532 (CPU @ 2.8GHz)
Sync 2: http://wprime.net/score.cgi?id=14533 (no change...)
Sync 4: http://wprime.net/score.cgi?id=14534 (ok its not that)
Threads were in sync already though (even in the standard syncing). Maybe the single syncing isn't enough for quad threaded systems, but its enough for my little dual threaded box. Anyways, try the above, if its a sync problem then that should fix it.