I know exactly what your problem is because I dealt with the same thing last night. The solution is pretty straight-forward, but you have to do a little digging first. The cause of the problem is due to Magento moving some of the upgrade scripts from Mage_Catalog to Enterprise_Catalog. In advance of the steps below, it’s helpful to download a clean copy of 188.8.131.52 and 184.108.40.206 to compare them side by side to see the difference.
So, if you did what I did, then you took your 1.11 EE base code and copied the latest 220.127.116.11 code on top of it and upgraded. Then you went into a holding pattern like a lot of us did when Magento advised against deploying sites on 18.104.22.168 and 22.214.171.124 because of url rewrite issues and db locking, and you waited for the release of 126.96.36.199. Then you copied the 188.8.131.52 release on top of the 184.108.40.206/.1 code. That results in a few errant files that need to be cleaned up.
The following files need to be removed in app/code/core/Mage/Catalog/sql/catalog_setup:
And in app/codeMage/Catalog/data:
The logic contained in those 4 scripts has moved to app/code/core/Enterprise/Catalog/enterprise_catalog_setup/install-220.127.116.11.php
If you try to run the upgrade in this configuration, the Mage Catalog sql scripts run first and then the Enterprise sql scripts run second and error out because they are creating items that already exist.
So take a close look at the above make sure your installation setup scripts match a clean copy of 18.104.22.168 for the 2 modules listed above. Once you do that, re-run your upgrade and it will work.
Best of luck.