Hi Daniel,
I have the same problem on my system. Not only with Claws mailer, but
also with Firefox occasionally, and most often with an xfce panel that
runs in sys-net and shows me the weather and the network load.
The odd part is that the panel widgets display their popups even though
I never hover the mouse over them deliberately. The popups display
when I use the scrollwheel to switch desktops.
As you say, it is not easily reproducible, so debugging it will be hard
I expect.
Mike.