Adam,
Now I understand.
I'm not sure what the best approach is; my first inclination is to re-install the 1.09 patch and see if that clears the problem up. So essentially you are going backwards in the upgrade process.
Did you do the 1.1 upgrade immediately after the heli patch? as in you did not run the software after the heli patch? That might be a problem, although I'm sure others did the 1.1 patch immediately after the heli patch.
Since what you have is unworkable, and the other choice is to start from scratch... I'd redo the 1.09 patch and make sure I follow the directions on http://www.fsone.com/Downloads/Default.aspx
Let us know how it all turns out.
Scott