I ran into the same problem, and ended up removing the various bits of KoboLauncher then reinstalling everything. The problem is that I went through the process the first time without really following the instructions, while I followed the instructions to the letter the second time around. (I think that it's exploiting some sort of quirk in the system, so achieving the same end result on the filesystem isn't the same thing as achieving the same result functionally.)

Maybe you're running into the same issue?