Comment # 14 on bug 1202066 from Eric Schirra

Thanks Andreas for your feedback and detailed explanation.

I can't recreate the problem myself.
I don't have any problems with FileZilla.
There are no popups. Rebooting the system while Filezilla is running does not
cause any problems either.
So for me everything works exactly as it should.
And teo himself writes it has nothing to do with filezilla. 
So teo. I recommend you to set up a clean system in a VM and then try to
reproduce your problem.
If you manage it, please open a ticket at Upstream.
Nobody can help you here.
Sorry.