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Ok. I had not experimented with the system tray option in a few generations so I just did some experimenting. I am using the latest version of OSX with all updates.
With the system tray option off (not checked), if I click a window somewhere on the screen, the Calibre window disappears. It still is on in the Toolbar on the bottom of the screen (has little light beneath icon). If I click it on the tool bar it pops right back up.
With the system tray option on (checked), if I click a window somwhere else on the screen, the Calibre window stays were it was. I can click back and forth between the Calibre and the non-Calibre windows.
That said, the old problem continues if the system tray option is on, which is that if I hit the red button on the Calibre window to make it close, I cannot open Calibre again by clicking the tool bar icon. No matter how much I click the tool bar icon the window will not open. If I click the icon on the system tray, it pops right back up. Very weird behavior.
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