I enter the notes exactly as I am supposed to, but the door will not open. It seems as if no one else has this problem. I hope my copy is not broken. I have been wanting to play this game for awhile. If you know a solution please help.

Are you sure you count it right? As far as I recall, the skulls should be counted from the door's side, like that:

654321 X

Where X is the door, and numbers are skulls in order (not sure if there's six of them, but you get the idea).

Well, that approach worked for me, at least - whether your copy is broken or some such, I can't tell.
(if you have the GOG one, it shouldn't, though - well, not at this stage, anyway, I'm finding it impossible to beat the final trial, about to make my own thread about it)

UPDATE: I was able to get past the puzzle.