It calculates based on a curve.
You need more skill ranks to go from +1 to +2, and even more to go to +3, +4, etc. +5 is like 57 ranks in a particular skill group, IIRC.
EDIT: I can’t remember the exact numbers at which you get each bonus. You can check the skill groups in the STS documents, and you could either work out the curve with some math or look up the answer on Reddit.
Considering what happened, you may have to manually edit your stats to their correct altered values.