Depends on the code you're using, you could easily be using a compare and jump on result instruction that use a different number of instructions depending on the data it's fed. It's easy to correct for, simply and NOP instructions to the portion of the code that is executed too fast. Determining exactly where this needs to happen can be found by single instruction cycling through your code during the interupt where the jitter is present and when it is not.
If I'm not mistaken generally speaking the portion of the code where a compare instruction 'falls through' will be the shorter portion of code compared to when it has to jump to a label, 3 instructions sounds about right, so you just have to put a few nops immediately after the compare falls through to make it the same length as if the code jumps.