what do you mean by isolation or the servo pulses being irregular(do you mean the servos might be the problem)?
Isolation is a means to leave two circuits unconnected electrically, but allow for information (signals) to pass from one circuit to another. There are several types but include using light to send signals in an optocoupler (optoisolator), or to use magnetic field in a signal transformer or digital isolator. I have even seen a large 50 Hz 3 phase power source isolated from the 60 Hz 3 phase power supply by using a large motor to turn a large generator. In that case the signal was mechanically transmitted.
Here is a link you should have read prior to posting your question, but I'll you slide by on this one: http://en.wikipedia.org/wiki/Galvanic_isolation
It's not the best wiki page I have seen but least they took the time to include diagrams.
Your cell phone allows your parents to send a text saying to come home without you having to actually see your parents, so that would be called social isolator. Angry mom or happy mom, all you see is the words sent by mom. You don't see the upset look on her face because you're late for dinner AGAIN! You only get the clear, quiet, no-attitude message to come home. Same with electrical isolation; you get the signal without the electrical noise that is on the other circuit. Angry circuit or happy circuit, you only get the message sent. Motor (servo) circuits can be noisy (angry) and that noise interferes with the communication between uCs (mom) and other electrical parts (you).
My comment on the pulses being irregular meant simply that the pulses from the uC may not be the same distance apart or not the correct width every time the uC sends one. Maybe your SW is thinking about something else when it should be thinking about sending pulses.
I don't know anything about Ardinos so do not know how the pulse trains are generated. If they are generated by flipping bits in an interrupt routine then maybe you're taking too long in the interrupt and missing the start of the next scheduled call, or maybe you're modifying a variable that gets used in the interrupt when the interrupt gets called, so it's not the value you want it to be. Can't help you there.