I had the same issue this morning. I have SS installed and also X-Note, Verizon ported rom, and Knox Raid 2.6. GPS was working but would continuously run because it never got a lock.
How'd I fix it? Well I deleted each rom slot and reinstalled the rom. I did this one by one, rebooting and testing each rom as I re-installed it. It turns out that after I uninstalled and reinstalled the Verizon ported rom, the GPS signal was able to lock on all, even my stock rom slot running X-Note.
I thought it was PHYSICALLY IMPOSSIBLE for a rom to modify settings like this within safestrap to where the changes you make in one rom could bleed over into the other rom. I thought that was the purpose of having SS rom slots.
But...you learn something new every day. I hope you don't lose too much info, but this is what got me back up and running.