By default the Windows version of XBMC uses a DirectX mode that is fast, but which won't share the display with any other app. When another app starts it forces XBMC to minimise. This is why you're seeing XBMC minimise when you use Advanced Launcher.
niltron's suggestion is to configure XBMC to use a slower DirectX mode that doesn't suffer from this problem. To do this go to System settings, System, Video and enable "Use a fullscreen window rather than true fullscreen". However, as nilstron notes, you may find this slows video playback.
I thought Advanced launcher had an option to deal with this problem, though I've just had a look at it and I don't see any such option. A workaround would be to write a short batch file to run your app, e.g. to run Handbrake your batch file would contain:
Code:
start /wait "C:\Program Files\Handbrake\Handbrake.exe"
"C:\Program Files\XBMC\XBMC.exe"
The first line runs the app, Handbrake in this case, and waits for the app to exit. The second line runs XBMC again. When you run a second copy of XBMC it just sets the focus back to the first copy, so the end result is to maximise XBMC again. Now configure Launcher to run your batch file.