Well clearly one of the controllers or HDD's is not performing well.
Can you run a HDD benchmark on each of the disk? Other option would be to copy a large file (something ziped say) to another folder on same drive.
Other thing to check is SMART status on HDD's, but do the HDD benchmark first.
On my main drive, I have tried copying my 4GB music folder to my desktop.
Transfer rate was circa 25MB/s.
I have the secondary unplugged atm, so will reinstall that and try that one.