Just now, I approached Alph in Cranberry Copice, and "Get Emblem" was grayed out. Yes, my inventory was full. But when I dropped things, I still couldn't get the emblem. (I cleared one, then two, then three slots, trying again each time.) I had to give something to Alph to get past this. (Which means, I think, that the extra points were thrown away.)
Oh hah, there's bluto's post on the same thing. Whoops!