I tried to run cooling over the eroupters and it seemed to interfere with them (maybe magnetically?) ,so I just leave them as is. I'll have to hope the boards run at a decent temp though I've got a fan ready to try and place when they get here.
Was the fan you were using a USB fan plugged into the same hub (Assuming BES, not BEB) or otherwise on the same 'power circuit' internally? Could have been the power draw affecting the BE's ability to function under load (unless the fan was introducing electrical noise into the power lines for the BE's?)