Love MatterControl... But there is definitively some issues when subtracting. In my case, when you try to subsequent subtract more than one time the same element, the item disappears or the application status bar gets stuck. If you try to subtract from a mid complex item, same issues happens.
I tough that maybe have to do with objects that are grouped, but even when they are flattened, its impossible to make it work in 98% of the cases.
Code team... please solve this issue.