This is probably a really dumb question but I have to ask.
We setup a metatags file and include it in every page of the website in the header section. If I look at the source of a webpage, on our site, I see the lines of code in the include also. That is what you want. Do the search engines see it that way when they crawl a website?
For example we have a generic Title tag in the include file. If we want to change it we change it in the include file and it then is available to all the webpages of the site. If we want to override it for a particular page we put the title tag after the include.
Are we sure the search engines are seeing the code from the include?