Just in case that can help, here is how to reproduce in even less steps :
1) open thunderbird.
2) maximize it if it is not
3) minimize it
4) open any non maximzed app, or else unmaximize the app (say firefox)
5) open thunderbird from message indicator
==> no need to minimize firefox after step 4, having it non maximized is sufficient to make the misplacment happen.
Just in case that can help, here is how to reproduce in even less steps :
1) open thunderbird.
2) maximize it if it is not
3) minimize it
4) open any non maximzed app, or else unmaximize the app (say firefox)
5) open thunderbird from message indicator
==> no need to minimize firefox after step 4, having it non maximized is sufficient to make the misplacment happen.