My guess is that your belly cord (retrieval line) is windward of the foot of the sail on starboard and leeward on port tack. If that is true, what is likely happening is that you are splitting the foot of the sail in half as it enters the snuffer… sail bunches up and keeps it from straightening out in the length of the snuffer. If this happens you are left with roughly half the foot length of the head that can no longer be pulled in.

You need to make sure the patches enter the snuffer first, not other parts of the sail bunched up in front of it. Try releasing the halyard and sheet while keeping it sailing hot so the sail inverts before entering the snuffer.