tried dragging the bottom right corner?

Thanks, I see now that there's a band along the bottom of the window that allows me to move it, but still can't figure out any way to resize it. (Neither bottom corner appears to have resizing functionality).

Did some more searching, and tried closing Thunderbird, deleting xulstore.json in my profile folder, then restarting Thunderbird. If I then open a "Search Messages" window with the main Thunderbird window NOT maximized, the "Search Messages" window that comes up is the "normal" default size that I'm used to seeing, and I can switch back and forth between the main window and the "Search Messages" window. If I instead maximize the main Thunderbird window and then open a "Search Messages" window, the "Search Messages" window at first comes up in the "normal" size mentioned above, and then maximizes (on its own/automatically). I am able to access the close/minimize/restore options in this window, though if I "restore" it, the main Thunderbird window ends up being hidden, and the only way I can seem to get back to the main Thunderbird window is by closing the "Search Messages" window. This behavior seems to me as though it must be unintended/a bug.

dugq said

Since upgrading to OS X El Capitan, the Thunderbird "Search Messages" window is performing differently. When I open a "Search Messages" window, it comes up almost maximized, and the only way I've been able to find to get back to the main Thunderbird window is to press the "escape" key (which closes the "Search Messages" window. Prior to upgrading to El Capitan, I was able to have multiple "Search Messages" windows open at once and switch between them and the main Thunderbird window. Thanks for any advice on this.

The problem is the 'default' windows size vis-a-vis the main window and your display. In Windows 7 the solution was to right-click on the top of the search bar, and open the window 'size' option, then using the cursor down, then [cursor right or left] keys to re-size the window. The 'problem' has been the peristance after you shutdown, and the screen does not 'remember' what size it last was.

It seems that there is a 'corruption' issue with a file that contains the settings, and where the file is stored, and does it get updated (written correctly back to disk) before you shutdown.

See this MozillaZine Article here: MozillaZine:Search window size always bigger than screen[solved]

A Screen Image would help, with a picture of the element that has changed with upgrading to ElCaptain! (OS-X).