I just tried, ignoring the "Done" button, and simply closed the customization pane with its X in the titlebar.

It also worked with alt+f4, another standard way to close a window. And also via the left-hand corner icon.

In each case, my customizations persisted.

So, I'm not sure that, worrying as it is, that the absence of the Done button is actually at the root of your problem.

Does it behave better in Thunderbird's Safe Mode?

https://support.mozilla.org/en-US/kb/safe-mode-thunderbird

This will eliminate add-ons as a possible cause.

And, which platform are you on? Windows, Mac or Linux?

I have the same problem in safe mode. The alt+F4 button did not help. There is no X in the title bar. I am running OS X Yosemite on my MBP. However, I tried it again. The customize toolbar window always opened in the upper left hand corner of thunderbird mail. I could not resize it or move it. I say a small line down in the lower right corner of the customize window where the DONE button would be. It was just barely visible. I managed to get enough of it to click on. The window closed and the icons I had put in the toolbar were still there. I cannot move the icons in the toolbar to where I want them, but that is ok for now. I still want to find out why the customize window does not open completely, and I cannot move it. I am wondering if the display option that I have set on my desktop has some effect on how windows in some of my other apps display.

Ah, you're a Mac user. We have had a sprinkling of display-related problems reported by Mac users.

Your best tactic right now might be to revert to an earlier version of Thunderbird.

https://ftp.mozilla.org/pub/mozilla.org/thunderbird/releases/

I did not go to a older version of Thunderbird because I don't know if the Theme Font Size Changer would work with a older version. I did finally figure out a work around for the issue, but I can't explain it in terms that someone else might be able to move. I found that if I keep moving the mail window itself to the right, until I see where I want to add the icons in the tool bar, the customize window moves to the left and the done button shows up. Then after I drag and drop the icons I want to use, I just click the done button, and things seem to work ok.

Forgot to say thanks for your help.

You should be able to drag the top of the customise windows down to make the overall height less. The same goes for the left and right borders. These changes appear to be saved.

So make it the size you want.

Thanks: That is one of the issues I still have. The customize window would not move or open to a larger size. Usually I could put my arrow in the bottom right corner and resize the window. But that does not work. The only way I was able to see enough of the DONE button to click on was to move the mail window over to the right. the customize window would also move with it, and then automatically move back to the left upper corner on its own. But then I would finally see just a small line in the lower right corner. I knew that is where the done button should be, and I was able to click on it.