Default character set
The default character set for a new document has influence on opening an existing .ufo. This shouldn't be the case. It should only have influence on newly created ufo's.
If I'm right RoboFont adds empty glyphs to existing ufo's in case the default character set is larger than the character set of the ufo.
(I experienced a couple of times that once the default character set is bigger than the character set of the opened ufo, RoboFont doesn't generate the ufo anymore).