I've checked all the altitudes related to runways and approaches in the AFCAD, and they looks correct. You can verify this yourself, by opening the AFCAD (there are TWO AFCADs at O'Hare, one contains the airport, the other the approaches), and see that all runways, ils and procedures are set to the correct altitude.
Fact that nobody else ever reported this in the 3+ years O'Hare has been out, seems to indicate it's not something that is related to the scenery, but something else you have installed.