Key detection is calculated by the software and the accuracy depends on how good the algorithm is written. That means that when you change software and re-analyze the tracks some of the key results will differ. It does sound weird that all keys have changed though.
Tip: Choose your key detection software and use only that one, do not switch between different apps. They all have their flaws, but if you use the same one on all of your tracks you will have less problems with key clashes etc. since you use the same algorithm.