Most likely something in the content of one of your custom templates is causing an error that prevents it form loading the templates. It could be a server side error which would show in the log or it could be script error which may not show anywhere if it is inside a try catch.
You can check the log for clues and you could backup your custom template to a text file and then delete it and see if it solves the problem then you will know if is something about the content of your template.
The older FCKeditor uses xml instead of json and may possibly be a little more tolerant.
Hope it helps,