[color:"orange"]Could it be because I stored the 2nd pyramid in a chest?[/color]

Yes, that will prevent you from using the teleporter pyramid you have with you.
There are several ways to get out of the easter egg area. In your case the easiest methods would probably be the following (save under a new name first):

Use the trick in the following topic to temporarily transfer yourself out of the area, head to where you stored your second teleporter stone, remove it from the chest and drop it on the ground somewhere, then save and restore the original data file. Try not to interact with anyone, complete quests, etc. while you are going to move the teleporter stone.
FIX for the Missing Catacombs Portal

or

Teleporting Anywhere, via hex editor



in general:
a way out, if you're Stuck in the Easter Egg Area (broken links are fixed in a reply)



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