I have had issues with other components of ArcGIS, specifically Server, where I installed SQL server native client after ArcGIS Server was installed and it wouldn't let me create a data store connection. I had to completely reinstall Server to fix this.
I wonder if the same could be said about Desktop. I would try reinstalling ArcGIS Desktop to see if it would fix the issue.
Also, I have been told repairing operations only replaces DLL files and such and may not fix the issue.
-Steven