Not sure what "out of sync" means either. I doubt the transistors are causing much of a problem and the original idea/suggestion was to ensure that the transistors were driven hard enough to light the LED's. A schmatic/drawing would help if possible. Just an idea, maybe using "HPWM" to set your frequency might help? Perhaps even a combination of "HPWM" and "pause"? Yes I was talking about using 2 transistors. My guess is that you are placing your LED's on the emitter side of the transistors and not the collector?