Wait... maybe I just have things plugged in wrong... I'm not sure now.
The cord on my fan, that can't be detached from the fan unit, is a 3pin yes... but inside the fan packaging there was a 3-pin to molex adapter.
Initially, since no instructions were included (with literally anything), I attached the fan DIRECTLY to the fan controller. The fans didn't spin at all when I did this, and the system quickly went in to a reboot loop until i powered it down. I therefore used the 3-pin to molex adapter, plugged the fan in to the adapter, plugged the adapter in to the PSU (using the molex interface). Now, the adapter also has an additional 3-pin input on it, so I used the extension cables included with the lamptron to connect the controller to this 3-pin input on the adapter.
If you can't imagine it, I'll take pictures in the morning. You're saying though that I should be able to plug the fans in directly to the controller?