I'll try and repeat the problem, so far , all I can say is it starts to happen when I've been using MOI for over 1hr, when I work, I do a lot of Undo's and I'll take an object I'm working on make a few copies and try different things on, so my files can grow quite large to I delete all temp objects.

I'm also have MoI set to mm, and tend to work on objects under 200mm

Some of the other things that start to happen, I might try to union 2 solids and , in stead of 1 single solid, it ends up removing 1 solid.

But I can't 100% rule out user error, has I'm been using MoI less then a month with no back ground in modelling software :)