Smuxi

This sounds like fvwm is taking the window urgency flag too serious, which Smuxi sets to inform the window manager that the user is supposed to react to a message highlight. Common window managers usually highlight the application icon by blinking or glowing but is not moving the focus, only if the user clicks on that window icon.

Too bad the specifiction doesn't say what purpose the flag exactly has and how a window manager should or could implement it. Changing the focus and virtual desktop sounds a bit too much for me though, but I am not a window manager hacker :)

If fvwm has no option to change that behavior, I could make it an option in Smuxi to disable setting this urgency flag.

[0] http://standards.freedesktop.org/wm-spec/wm-spec-latest.html#URGENCY

As the EWMH [0] is pretty vague what the urgency hint is about, the ICCCM [1] has more background on it.

This mechanism is useful for alarm dialog boxes or reminder windows, in cases where mapping the window is not enough
(e.g. in the presence of multi-workspace or virtual desktop window managers), and where using an override-redirect
window is too intrusive. For example, the window manager may attract attention to an urgent window by adding an
indicator to its title bar or its icon. Window managers may also take additional action for a window that is newly
urgent, such as by flashing its icon (if the window is iconic) or by raising it to the top of the stack.

[0] http://standards.freedesktop.org/wm-spec/wm-spec-latest.html
[1] http://tronche.com/gui/x/icccm/
[2] http://tronche.com/gui/x/icccm/sec-4.html#s-4.1.2.4

Looks like this is a well known issue with fvwm as they have an FAQ entry [0] with a solution for it:

cf9. Why do certain applications such as GAIM and XChat steal focus/switch pages/etc., at certain times?
There's a certain property within the WM_HINTS XAtom that, when set, causes the specific window to get top priority via
the window manager. It seems Gaim and XChat do this to denote the fact that someone is explicitly referencing your IRC
name, for instance. For some people this can be very annoying, and thankfully there's a few things that can be done
about it. Whenever a Urgency hint is set on a client, FVWM notices this and immediately executes a built-in function:
UrgencyFunc as described below. ...

Can you check if that solution works for you? If so, then we can close this ticket.

[0] http://www.starshine.org/xteddy/thomas/fvwm/fvwmchanfaq.html#cf9

Perfect. Many thanks.

Adding
DestroyFunc UrgencyFunc

at the end of the fvwm configuration fixed the issue.

(thanks again, I hasn't been able to find it on the web).

If I may, you should add it to the FAQ.

As the issue is solved outside of Smuxi I am closing this ticket now