As you can see in the attached screenshot of my desktop (XUbuntu 12.04
32-bit), when exiting a conversation that has an ongoing file transfer
the popup window is borderless, the confirmation buttons are not
displayed and the user can't do much more than blindly hit "enter" and
hope the right button is hit.
Similarly, when I attempt to close a chat window that has had a recent
incoming chat message, I get a borderless (and mis-sized) window that
has very similar characteristics (expands beyond visible desktop,
can't see the buttons to click).
I believe this qualifies as a GUI bug.