I have seen the same issue with 1.40 and 1.4.1. After the program has been running for awhile (after a OS restart), the right click menu goes away and does not come back up until NWARE is closed and re-opened. Once this happens it continues to happen about every 5-10 mins until the OS is restarted.
I noticed this happening when I am copying and pasting (ctrl + d) controls from a device (level control) then I right click for control style paste.
Also I have seen the TAB bar disappear In the lower left tool bar the tabs that say Devices, Flyoffs, Scripts, Media and Inspector disappear. It will come back if I click in that general area where the tabs were.
Side Note: Any plans on adding Keyboard accelerators for Copy/Paste of control styles?