I would swap the HDD and the SSD and see if that does help. I sort of doubt it but it's possible. My SSD is in my MP and it's still as fast as ever. I've even filled it to 140 GB, although that was temporary.
I've done a ton of copying to and from my Time Capsule, filled my SSD, deleted stuff, wiped out and restored my iTunes library, done two boot camp partitions, run VM Fusion, uninstalled Fusion, and more. And it's just as fast as it was when I first installed. Boot up still takes 13 seconds. Although I'm using an OCZ drive - but it shouldn't be that much different.