Because it's not always just offending PROGRAMS. Sometimes another process happens to be running and screws up something extremely minor, like some random GConf setting getting set/unset, or whatever - this isn't always handled by the offending program, but usually by the preinst/postinst/prerm/postrm scripts of the .deb file. And the rm (remove) scripts don't always account for some rare mistake that could occur in executing the inst (install) scripts. And the reinstallers of other packages (especially stock packages) are likely to assume that everything is already fine and dandy and correctly set on the system.

However, in the case of the vkb, something like ukeyboard might, since it modifies the vkb (not sure how, never used ukeyboard), modify the relevant files/keys/whatevers, and so when it uninstalls, it resets them to defaults. Or something like that.

There's a pretty big shitload of possible ways something could go wrong, and that means that invariably you're going to encounter problems that don't reset with a simple reinstall of broken packages, but might fix with some other messed up mix of steps.