Update
All right, I think I know what's happened...
The Addon Manager section of the XML file was missing the optional tag <ManualLoad> so, the Uninstaller wrongly assumed that a section should be 5 lines of lenght (our installer puts 5 lines, in fact), when in fact it might be also 4, if the optional parameter is left out...I guess Cloud9 or Aereosoft installers probably didn't use the optional line.
Due to this, the Uninstaller deleted 1 line more than it should in this cases.
All right, I've just fixed the Uninstaller for both Zurich and the stand-alone Addon Manager, should be available shortly, the time it takes to upload to the servers.