When playing with the internal test build (with cari's changes), i beleive it will keep the ship selected until you go and physically click on the next ship you want to move. I'm not sure about a beta version, though with the Mods stuff it'll probably be necessary, but we'll see how you guys like the current implementation of "No Auto-Focus" and see if it's what you're looking for (but FYI, it fixed all my problems with the feature).