You're doing something wrong...
You shouldn't be calling any templates from anywhere manually.
Don't rename those files, the system uses them. If you renamed them in your skin folder, then it's ignoring it and using the ones in the /core/templates folder. DON'T rename anything in there.
Huh? None of the templates have a header or footer. There is a master header/footer.tpl in your skin folder that's used. Roger's video tutorials show those of these. Templates are automatically called, 90% of the time you don't be touching any of these, and there should be no manual template calls at all.
Just put your header in header.tpl, and footer in footer.tpl. That's ALL you should be doing for now. Delete any templates you put in your skin folder, and just follow the header/footer directions, and then follow:
http://phpvms.net/docs/skinning#skin_elements
To add those pieces into your header.
Watch Roger's tutorials again, I think there's a misunderstanding about how it works