I have a fresh installation of 3.5.1 and the latest CCTM.
I have created some Custom Content Types with Relations.
The problem: Nothing shows up in the thickbox while clicking the Choose-button while editing a post or the Set Search Parameters in the settings area.
In other areas the thickbox seems to work and the relation.js in the wp-content/plugins/custom-content-type-manager/js
Im using the latest FF but have tried it in IE as well.