Multiple reasons, but mostly it's because you freed up the cpu to actually work, instead of waiting on data from a far slower hdd. You went from running as fast as you can, uphill, to as fast as you can downhill, there's going to be some differences.
Also depends on how exactly you did the swap, whether you kept the hdd as backup storage, whether both were hooked up at the time of windows install, whether motherboard drivers are native or windows versions after a reinstall etc. There's plenty of possibilities.