I have been having the same problem, I beat the game with you and Ultrawolf, once with your copy and once with mine. It does not auto-potion with Ultrawolf either. Maybe after you beat it they make it harder. I feel your pain tho, it stinks!
I've found that when your partner is alive in co-op they're auto and when he's dead they aren't auto so maybe on single player due to lack of partner you have to potion yourself
@ regnisab:
From all the people I have talked to about this, that seems to be the case, erm. Apparently you only need to have an achievement w/ Alien Hominid HD also, to be able to use him, you do not necessarily have to own it.
I could swear that my potions worked automatically when my partner was dead in coop. Not sure about single player, I only played the first 3-4 levels by myself and I never died.
They should increase the amount of potions you can carry in single player then ;)