I think you're beginning to learn a painful lesson on why you don't produce a PCB in large numbers until you've had a chance to run it through the wringer for a while. 
You know what they say ... in theory, there's no difference between theory and practice. In practice, there is. Having a schematic and a prototype that works is only half the battle. (Guess how I know...)
I agree with you that the noise is probably not caused by a ground loop. Trying to alleviate the noise using techniques intended to fix ground loops is just going to be a waste of time. There were some good suggestions a while back on trying to isolate the high current loops using capacitance and such. Did you try that? I know it's not what you want to hear based on board layout, but if you can, test the theory anyway. If for no other reason than to prove it wrong and move on to something else. Do whatever you have to do to get a large cap on the power rails near your LEDs and see what happens.