is it low bar squat then? I've never squatted much with it but it wasn't fun when I did. I think he teaches that vs high bar squat to emphasize sitting back into the squat.
this is part of why I don't like SS. how are you supposed to address weaknesses and stay within the confines of the program? for instance, I knew my erectors were a weak point coming back from my injury so I do GM's after deadlifts. a few months later, problem solved, my back is stronger than it's ever been.
I suppose you can choose to stick with it, or ditch SS for something else that lets you address your weak points unless someone else has a better idea.
a lot of people DO say to stick to a program, but that's because so many people have program ADD and fail to progress as a result, not because the goalposts keep moving back (as they should) but because theyre all over the place. however, I totally agree with Bonez' advice that you should do whatever it takes to progress. if you feel that your lower back being sore is keeping you from progressing, I'd change things. if you can still make progress, then keep on keepin on.