Hi Steve - so your main base piece has become a "Joined srf" instead of a fully closed solid - it has some openings in it and booleans will behave differently when done on an open surface object instead of a closed volume.

You can see whether an object is a solid or not by selecting it and then looking at the type indicator which shows up in the properties panel in the upper right area of the model.

I suspect that your problems are coming from having 2 cut out areas just kind of exactly graze each other along a shared edge in these areas here:



By having those 2 adjacent recessed areas exactly graze each other at a shared edge like that, it would basically require that one edge there to be shared by 4 neighboring surfaces instead of only being shared between 2 adjacent surfaces. That's called a "non-manifold" edge and MoI tries to avoid making those kind of edges - when a boolean result would cause a non-manifold edge it tries to go through the model and decompose it into different separate chunks so that there are not any non-manifold edges in it anymore - it's that process that is likely causing you problems.

It's usually best to avoid creating things that exactly graze each other in such a way to make that kind of non-manifold situation - is it possible for you to slightly shrink the cut out area so that there will be a tiny bit of area between the corners of the 2 recessed spots?

You might kind of think about the current exactly abutting recessed areas as having created a zero width area of the model (at the shared edge) and that's what you will probably need to avoid to make it work well.

- Michael