I've been constructing an example of an "open source" rapid prototyping machine. The guy driving its development is a scientist, Dr. Adrian Bowyer. Some of his team are using an open source modeling program called Art of Illusion, and he's written a page giving hints on getting the best results from it. He points out that it gets the same sort of "it does not compute" message that we get in TC resulting from degenerated booleans, and in addition to showing how to avoid it in AoI, gives an explanation of the reasons why it results from the mathematical operations that CAD uses. Some of you might be interested.
The AoI page here: http://www.reprap.org/bin/view/Main/AoI
The maths explanation here: http://reprap.org/bin/view/Main/SeparatePageOnTheQuestion