I'm not exactly sure what you mean by "custom template", if you're referring to the initial setup of DNN, I don't recall what I used (it was a looong time ago), but I would suspect I started with the basic portal template, that is what I've been doing with all sites I setup.
I have another parent portal setup that I installed the module on, and it does exactly the same thing there. However, I just tested it this morning on a "child" portal I just created a day or two ago, and was working properly on that one, so I'm thoroughly confused. Both of these other modules have literally nothing on them, using the DNN Blue skin, etc...
Nothing at all in the logs, no error messages on the screen, I get a basic "empty" DNN page, menu across the top, copyright across the bottom, but no table whatsoever in the middle where you usually see TopPane, LeftPane, CenterPane, RightPane, BottomPane, that table is missing entirely.