When I left click in ZBrush using a Cintiq it seems to register as a click and drag. So if I ctrl - shift - click the background to unhide the whole mesh, it will invert what is hidden as if I performed a click and drag. Using a tablet, mouse, or trackpad, instead of the Cintiq, works just fine. Has anyone else had this problem or found a solution?
Update - Solution
After sleeping on it, I figured out what I did. Instead of Disabling RightClick Popup (Preferences > Interface > Navigation > Enable RightClick Popup, I decreased Click Time. (Preferences > Interface > Click > Click Time)
I did this so the Right Click Menu would not come up while navigating. Hopefully this helps someone else who made the mistake I did.