When you switched it to the Intel Sata II ports, did you also installo the latest Intel drive which performs beter than the default msahci. Intel driver is iaSTor and should be 10.5 or later (i think they are up to 10.8).
In adition to being on the marvel controller, I believe that is the OLDer controller which compounds the issue.
Added when switching from the marvel controller to the intel Sata II (you probaly did but would be remise if I didn't mention) you shoud do a secure erease and that means you have to do a fresh install. Note also if you run back to back benchmarks performance will suffer untill trim & CG have time to recover the drive.