Thanks for using Auto Thickbox Plus, and sorry for late reply.
I don't have cMap-Template of Connections (it's not free), so I can't debug the plugin in reproduce environment.
But I guess this problem caused by iframe function in auto-thickbox.php. Please try to modify auto-thickbox.php at line 55.
* iframe function is defined by Auto Thickbox plugin (not Plus). I think this function is buggy.
The plugin has the possibility to deactivate the re-writing of the links on text links. Unfortunately that does not work.
"ThickBox on Text Links" option targets links to image (i.e. link URL ends with image extensions).
But links like "Show Map", "Show Bio", "Show Notes" and so on are not linked to image (link URL may be only "#").
This is the reason why this option does not work.