I hear you. I can only apologise and cite a heavy workload at the moment...

Regarding menus showing up on a page in a new template - I wonder if this is simply because the module positions are different on the 2 templates? Your original one might have your menu showing up in a position called "top", whereas the new one might not have a module position called "top" at all (it might me "advert1" or something else, in roughly the same position).

If that's the case then you'll need to edit the second template manually (sorry to say - hacking through the template's index.php and possibly other files in the template) to find and change the name of the module position so that the 2 templates match.

Do you think that could be the problem? If the template is being switched then MetaTemplate is doing its job, but the naming and positioning of module positions, and matching these between 2 different templates, is a different matter (and out of the scope of MetaTemplate).

Hope that might help,
Stephen