Perhaps this is a result of a cancellation of the tool length offset? Haas is pretty convenient in this regard, as it has a couple of different systems to reckon the tool length offset.
I am not sure what kind of tool change macro the Mits uses, but you might try adding in a return to Z home before you call for the next tool. This should lift the tool well up and out of the way so that if it does a curtsy, it won't hit anything.
Another possibility to check for, would be a parameter setting which affects whether the tool length offset executes as an immediate discrete machine motion, or whether it combines with the next movement of the axis. I know Mits lathe has a parameter to this effect, don't know about mill.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)