That is wierd.
I am playing through the game on ng+ myself right now to test the new stories, quest and areas, so i will take a look at the squirrel story as well.
From what you described i may have an answer but i need to look in how i programmed that quest to be sure. It could be that the game is counting the acorns collected in that area and not the ones actually in possesion, will check later today when im back, if that is the case.
Thanks for ketting me know^^
Edit: It's fixed now!