I run the zim desktop wiki (python/gtk) http://zim-wiki.org/ in a workspace, and rss readers like akregator (kde) and quite-rss (qt) https://code.google.com/p/quite-rss/. From these applications, I ask to open a URL. This will launch the browser, firefox (gtk) or rekonq (kde). If I keep the browser minimized and in another workspace, then there the the browser will open in the buggy state. Some combinations work systematically at my place (calling firefox from zim), some are not systematic (calling rekonq from quite-rss). I think it can as well happen if the window is not minimized in another workspace, but the probability of the bug is lowered.
When a window enters the buggy state, it cannot be raised on top of other windows. If the window is raised from taskbar, it will open at a layer below Normal. But it actually does not behave like a normal window. If I change the layer to another value, say Top, then it will obey teh setting (and will be on top of other windows on he Normal layer). But as soon as there is another window at the same level, the buggy one cannot be raised on top of the other one. Actually, if the buggy window happens to have the focus, it will indeed be on top. When it looses the focus, it cannot be raised on top anymore (until layers of both windows are changed again to something else).
Now the very annoying part: when such a buggy window is minimized to the taskbar, it cannot be raised again and has to be killed from a terminal (with possible unsaved data loss).
It might or might not be related to bug #1084 https://sourceforge.net/p/fluxbox/bugs/1084/ windows don't raise from tray