Chris: The menus (main menu, campaign setup, etc) are drawn on top on the XFire window, anything that can be done there?
Unfortunately, no -- the menus and such are GDI, versus they are hooking into the Direct3D windows. There's no way to blend the two modes more than what I am doing, they are like entirely different windows on your desktop in that sense. So I would expect drawbacks like that, but it's only with the lobby and main menu that this would mostly be an issue. During gameplay it should be fine, there's no GDI unless you hit Escape or bring up the Stats window.
Similarly, tooltips are still displayed as the mouse pointer moves around the XFire overlay. There's also an issue with the overlay suddenly disappearing during campaigns, which may well also be related to the way that many windows in AI War still seem to be accessible when the overlay is active.
I don't know what would cause that. Does it still happen in 1.201F? When the overlay is up, is the game supposed to not be accesible? I would presume that the GDI windows would not be affected by whatever they are doing, but that the Direct3D parts would be, so most likely that is what you are seeing.
EDIT: Excellent news! The hooks catch every time on version 1.201F, just 1.013 that has that problem it seems.
XFire only fails to hook if you start a campaign, then quit the game. XFire will hook each time without fail if you don't progress beyond the menus. If you wait approximately 3 minutes before relaunching the game the hooks will again catch.
That is strange indeed. Does it still miss catching when you load a savegame, or just after you start a new campaign? It might be that it is getting thrown off by the second Direct3D window that is in the lobby, trying to hook into that in addition to the main hook.