Hello Friends!
(using 5.1.1)
I ran into another issue now on which I am currently looking into.
I created a module package. and exported the template on which I have placed the controls of this module.
Now I am trying to test both module package and template into a fresh installation (5.1.1).
I successfully installed module package. Then I copied the .template and .template.resources files in _default folder. And I created a child portal using that template.
Issue is - i can see that all the pages are created in newly created portal BUT all those pages are not showing the module controls. Anybody having any idea OR am i missing something??

I can add module explicitly. BUT the pages which are added automatically (by the template that i selected) and suppose to be having the module controls are showing blank (without any errors)

Are there other modules that do appear in the pages?

I would create a template that uses, for example, an HTML module. If pages created with that template add the module correctly, then I would conclude that there is a problem with your module.

well, It seems it IS the expected behaviour. because:
the child portal which is created by using the "exported portal template" is showing the HTML boxes that i created BUT not showing the module controls that i added before exporting the template.
I figured out that .template file doesnt contain any information regarding custom modules that i added. it only holds default module information only that we add.

Does your module support the "iPortable" interface?  Does it do Export/Import?  That is required to be able to move content for that module using the template.  DotNetNuke should, however, create a content-less version of the module.  The custom module must be installed on the target portal first, however.