When I started Thunderbird and it requested the master password, the prompt almost immediately lost focus. If clicked on to regain focus it again lost it. The only way to enter it was to click and immediately type a letter (sometimes requiring several attempts for each character), then click and type again.
I finally found the problem to be a Windows utility program that I use, AutoSizer which attempts to size & position certain Windows on my machine including the main Thunderbird Window which forced the focus back to the main Thunderbird Window when the dialog box opened.
The best solution I found was to configure AutoSizer to only size and position Thunderbird when the "Local Folders - Mozilla Thunderbird" window is visible. Then when I need it sized and/or positioned I select Local Folders (a screen I hardly ever visit) and AutoSizer will then do its thing.
This one was a real pain and I am posting this to help anyone facing a similar problem. Surprisingly on my Windows 7 system this never happened using the same versions of Thunderbird and AutoSizer,