Did you ever have the 1.33 patch installed, and maybe ran into the black map bug?
Long shot, but try deleting all of the files in the '..\Divine Divinity\Run\Dynamic
This folder is used as a cache for the game. Files are created / copied there from the save game folder when you load, and written / copied from that folder when you save a game. The files will be re-created as required the next time you start Divinity. If there was a corrupt file in that folder, deleting the files should fix the problem.
Then if you have a recent save just before reading the parchment, try that, otherwise just try again with your latest save.
The lower levels are optional, but you can get past the stairs with;Teleporting Anywhere, via hex editor
= 40 6F ; Y
= 70 D9 ; map
= 00 - Iona's dungeon, level 2, at the stairs from level 1