I encounter this problem with Media100 & RED on a daily basis.
It doesn’t actually lock up the Media100 system. It just prevents you from switching windows within the Media100 environment.
You can still trudge along and complete whatever you’ve been working, save it, etc. if you tap dance between your Media100 windows and the desktop. You can even quit and work on other Media100 projects.
If you want to select a certain Media100 window, click on the desktop first and then the window that you want, timeline for example. Then if you want to go from the timeline window to the bin, first click the desktop and then the bin.
This workaround doesn’t make the bug state go away but permits you to continue working. Some shortcuts don’t work in this state but you can still work. To remove the bug state, you will need a force-quit.
The bug state seems to be tied to the switching of tasks between the Media100 app and the RED app, handing things off from one to the other. By switching the active app from Media100 to Finder & back, you can jump from one Media100 window to the next. If you stay within the Media100 app, you can’t traverse windows.