I'm also running Debian/Sid (so same versions of everything). I'm seeing
a different behaviour, which is quite funny. When I click on a
thunderbird email on beagle-search, thunderbird does shows me the
correct email, but not a single window, but in the three panel window
(so the message is in the bottom right panel). Interestingly, the top
right panel, which should show a list of the other messages in the same
folder is empty (!!).
Also, it opens the message in a new three-panel window every time (of
course, this would be fine if it were opening the message in a single
panel window). So in my case, Thunderbird is not brought to the top if
it is already running.