When clicking on the cross of a window to close it, when that window doesn't close, a message pops up to say it is probably not responding. Unfortunately this also happens when you do this to konqueror or firefox with multiple tabs open and warning about closing multiple tabs enabled. Same thing happens when closing kate with unsaved changes.
I filed a bug about this at https://bugs.kde.org/show_bug.cgi?id=129410 but they believe it is a distro patch which is causing this.
In general we do not include custom patches and there's nothing that would relate.
I've rarely seen such a message popping up on systems under very high load, so if you experience such messages regularly, you might have processes going crazy, causing high cpu usage, maybe together with swapped out memory, which causes your application not to react timely.
As you've pointed out in the upstream bug that this is not an issue for you anymore...
I didn't think Gentoo included any patches causing or any other patches for that matter, but it is good to have confirmation :)
Sorry for forgetting to close this bug.