The reason for this is that a computer is only as fast as its slowest component!
One of your machines may have a much faster CPU, a shed load more RAM and a faster bus speed, but all of that is nearly worthless if the hard drive only spins at 5400rpm and can only move data from the drive to the processor at a slow speed!
Mathmatica is quite a drive/swap intensive program - it needs a fast hard drive. If you put a 15k drive - or better yet, an SSD instead of a 5.4k in the faster machine, it would absolutely fly!
Its the same as having a forumular 1 racing car, but sticking it on a 30mph road - you still have the fastest theorewtical car - but its worthless if the road is limited! (weak metaphor, but I haven't had a coffee in a while)