One thing that I need to try is to replace the hammer spring with the factory spring. Three things help to arrest recoil. First, weight of the slide eats up recoil energy and then the recoil spring burns up a lot more recoil energy. Third, the hammer spring helps to slow the recoil too and I've not been taking that into account. I read earlier tonight about someone having an issue with a new CZ in .40 and described it as having "a 50lb trigger". If CZ used a heavy hammer spring to help tame the .40 round, it could explain why I'm having issues with mine now that it has a lighter trigger spring.
It sounds like you are onto something.
Also....did you mark the mags that were in the gun when it was having issues.
You know the drill. Run that mag in another .40 if they are the same and see what it does. If it runs then repeat in the problem child.