On GNU/Linux Debian ubuntu 13.04 (32bits or 64bits), using the official 3.8.1 claws mail or the PPA 3.9.1 claws mail, the window managers (gnome 3 or unity or openbox(lxde)) do loose some popup windows. Have to kill the application.
To reproduce, try to configure a filter, you should "loose" a popup in the process, the popup is unresponsive and you are then stuck. It did happen for several different popups.
re-opened because I modified the wrong bug report!!
Tried with lxde and Claws 3.9.2 and it works fine for me.
I suspect that, if anything, it's mishandling of modal windows in unity, and that rather than losing a window it's actually a modal window that wrongly goes behind another window, thus making the presented window appear to be unresponsive.
This is not specific to unity. As I wrote down, it seems all window managers are affected. What I forgot to write down, sylpheed (the "other one") is affected by the same bug (evolution is not).
I saw what you wrote but, nevertheless, not all window managers are affected. Of the 3 you listed, I tried lxde and could not reproduce the problem.
evolution is gtk3. sylpheed, like claws-mail is gtk2.
Then it would be GNU/Linux Debian Ubuntu specific, with high suspicion on their gtk2 build.
This report could be relevant:
Do you have the overlay-scrollbar packages installed?
Tested: popup windows now responsive after full overlay-gtk removal.
moving the bug to proper faulty components.
*** Bug 2920 has been marked as a duplicate of this bug. ***
*** Bug 2694 has been marked as a duplicate of this bug. ***