I have had success with the standalone Coot, found here: http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot
It doesn't use the Fink package, which seems to be part of your problem. Try completely uninstalling your version and reinstalling this one. I've had no problems at all, though it did take Coot a minute or two to start once I upgraded to Mountain Lion.
