I just can't think of a way that the FC could cause that though. The circuit is very simple - motor signal comes right off the pins on the processor so there's no components to fail.
The code is pretty simple too, at arming all four motors are given the same signal.
So the only place a variation in start up should be coming from is the ESC's.
Now, there could be a bad pin on the processor - but that would almost always present as a totally dead pin.
The only thing I can think of is possibly an intermittent short or iffy solder connection. You could try reflowing the solder joints on the header pins - and if you've got a good iron and steady hand you could try reflowing the pins on the processor for motor out.
The code is pretty simple too, at arming all four motors are given the same signal.
So the only place a variation in start up should be coming from is the ESC's.
Now, there could be a bad pin on the processor - but that would almost always present as a totally dead pin.
The only thing I can think of is possibly an intermittent short or iffy solder connection. You could try reflowing the solder joints on the header pins - and if you've got a good iron and steady hand you could try reflowing the pins on the processor for motor out.