In case some poor soul goes searching the forums for the problem I had, there are many ways it seems that combine operations can be screwed up. One is where it actually works but looks like it doesn't. If you want to JOIN bodies with the Combine tool, make sure you UNCHECK "keep tools". If you don't what will happen is the bodies will join as you commanded, but the original bodies you used, the "tools" will remain. First, this means that all the bodies you wanted to join will stay in your browser and make you scratch your head saying "why the heck didn't it work???" Second, it means that you will have, in effect, two copies of the same shape perfectly "phased" into each other, which is extremely difficult to see unless you zoom in real close - then you will see some aliasing on the lines. Its even hard to see with Inspect >> Section Analysis, but you will notice some wonky "half lines" that happen when its trying to show both the joined body and the "kept" body at the same time.