I also have this problem and am guilty of simply being to lazy to report it.... Now that someone else has thrown the first rock... I am happily joining.
Most of the time when I try to achieve something similar I have success when I preform a boolean diff 'one by one'. Selecting many objects at once leads almost in any situation to funny results.

Even when all is well, firing off a 'multi diff' is most likely to result in some sort of strangeness like parts are vanishing, or the inverse of what is expected happens. The wrong geometry vanishes and the unexpected results remain. Sometimes elements remain and have to be deleted manually to 'peel' the desired result out of the 'waste geometry'.

Once there is overlapping geometry all bet's are off. It is clear to me WHY but when it happens, based on the general lack of feedback by MoI3D, backtrackign to find the reason starts. A tiny overlap, almost within the numeric precision, is enough to ruin one's day. Again, a red flickering MoI button and/or a buzzer would be good enough to recognize that something fouled up. No need for a fully fledged exception handler with auto problem solving AI in the background (Homers Voice: Hmmmm AI......).
Lemo