I've noticed this anomaly using Psi, although once or twice it happened with another applications. The problem is with appearing of new dialog windows, being children of already running applications. The window (in my case the Psi chat dialog) pops up at the top of all windows on the current desktop, however it doesn't have a focus, thus after pushing twice <alt><tab> it's at the bottom of the current desktop. Before upgrading to 4.1.90 I was using a CVS snapshot from ca. beginning of the August and it never happened. It is rather minor problem, but it's a pain in the ass.
That's the stealing focus mechanism, the applications (or its toolkit) prolly don't update their _NET_WM_USER_TIME (and xfwm4 don't give focus to windows whose _NET_WM_USER_TIME is older than the last event time)
BTW, I've now added a new hidden option "prevent_focus_stealing" (disabled by default)