I found a problem eventually. There was a dependency in the bundle's DLL on one of the libraries, which name was changed during the Post-Build stage by install_name_tool. install_name_tool location was changed in Xcode 4.6, so this step was missing, therefore bundle's dll looked for the wrong library in wrong location.
I guess giving error like "Library XXXXX in missing" is too much for Apple....
Hope it will help someone someday.