https://bugs.launchpad.net/ubuntu/+source/thunderbird/+bug/196058

You can restore the windows border with these steps:

1. Close Thunderbird
2. Edit the file ~/.mozilla-thunderbird/xyz1234.default/localstore.rdf
3. Search the entry

<RDF:Description RDF:about=“chrome:messenger/content/messenger.xul#messengerWindow”

                 width="800"
                 height="600"
                 sizemode="normal"
                 screenX="5"
                 screenY="5" />

# Change the width, height and screenXY entries to the ones you see here

1. Restart Thunderbird and it should have its borders again.