[capidamonte]

Okay, I installed metacity. I do not have the rest of Gnome installed.

For this test, I'm quitting Calibre, then changing window managers, then launching Calibre with the --start-in-tray switch. (And only that switch.) I also click the book-browser button once the window is visible so that the tiny window is restored to full size and doesn't, perhaps, save its size when Calibre exits.

Under compiz: Launching calibre produces a tray icon and a blank window. Clicking the tray icon shows the window, and the tiny book-browser window in the upper left corner.

Under xfwm4: the same.

Under metacity: Launching calibre produces a tray icon, no window. Clicking the tray icon shows the window, and the tiny book-browser window in the upper left corner. However, for a moment, the window is blank before it changes to visible.

Under all three window managers, launching Calibre without the --start-in-tray switch works as expected: visible window, visible tray icon and no tiny book-browser.

Hope that helps somewhat.