This is, in fact, a bug! Must be a bug from the original, too, unless something *very* bizarre happened with Sara's coding.
Apparently, if you enter Time Attack mode, then exit it, THEN load up your savegame in Nightmare... SP gain will be normal! But otherwise, it's 1 apiece, no matter what.
No clue how something like this came to be, but we'll definitely look into fixing it for a future patch. Sorry for any confusion!