Fix the position of the hole that you don't want to move first (by dimensioning it from other sketch lines, main planes, model edge, etc.).
As glen says you need to decide which hole is the driving hole, it sounds to me like they are both able to move in some way and depending on how you change and rebuild the model is allowing the holes to move in an unexpected way, lock down the first and decide which hole is fixed in its location in respect to the other (i.e. which is driving the position and which is driven by the first holes position, ensure they are correctly dimensioned and defined and it should then respond in a more predictable way.
FYI if both entities are unconstrained then I think SW will always move the right-most entity, and if they are vertical then it will move the lower one.