All but 1 province was directly annexed to the vassal via the peace brokerage screen. In a couple of past games I've gotten myself into trouble (150+ overextension) because the vassal would not accept any more provinces and as a general rule try to avoid taking the provinces myself.Have you been always feeding him like this, or did you do it the other way too, when you take all provinces for yourself and then grant them some from the vassal interface?
I think it's a case of a lying/buggy UI, there is also a case where you are reconquesting for vassals, and the returned core province modifier only gets applied when you use the return cores tab in the peace deal, not the clicking directly because the vassal will automatically get it. But IRC the LD reduction is applied in the latter case, however if you switch it out to return core, you get the opinion but not the LD reduction.
I never use the return core thing (although now that you mention it, I surely should).