I had 1 PSU powering the boards and the controller. I put another psu on the controller and booted up the boards first, and now it is running at full speed. Thanks for the advise you two..

This makes you wonder if it would be worth installing a cut-off switch on the power cable that connects to the controller. This would be helpful if you are using a single large PSU...
Why would that matter? My guess is that the 1 PSU alone didn't have enough power?
Regarding adding multiple PSU's etc, I can recommend add2psu adapters.
http://www.add2psu.com/You could get these to power the hashing boards first, and controllers later.
I used them on my GPU rigs back in the day.
Edit:
DO NOT use these on multiple circuits!Are you sure about that ATCkit? I guess you are if you're doing it! ^^