Let me see if I can explain.

If you look at the position of the large staircase that goes all the way from the crypt to the top of the tower (K18 in the original module) as compared to the nearby one that goes from the dungeon upward (K21 in the original), you will notice that on the Larders of Ill Omen (and above) that the smaller staircase's center is in a different relative location to the large one. On the bottom level it is 10' west and 40' south of the larger staircase. On all of the other levels it is 30' west and 10' south.

The long hallway that leads from the brazier room doesn't also line up with the crypt that it comes up to. Here is an image that I hope helps explain it.

Click image for larger version.  Name: StairOffset.jpg  Views: 104  Size: 103.5 KB  ID: 81404

The 'too short' one is on the Court of the count, there is a long staircase near the north west corner that takes a turn up into the room with the 10 statues on the Rooms of weeping. This staircase shows that is goes 40' west, turns left, the becomes a half spiral at the end. In order for it to reach the destination shown on Rooms of Weeping it would have to go 50' West before turning to the left.