ive noticed exactly the same behavior. i tried upping the priority of mp to no effect. any ideas on how to workaround this?
"always on top" is a workaround, if you have a dedicated htpc, as it gets the focus always.
I hope MP2 will take a little more care for systems which are not only running Media Portal, since this one here isn't the only problem for a "second display htpc" (speaking from dynamic refresh rates and remote controls).