Site performs differently in CFM vs HTML on Chrome

Okay, so this is very strange. I have a site that I put into several ColdFusion docs for header / footer / etc. My site's footer is attached to the footer using a jQuery plugin. When I go to the index.cfm page (in Chrome) to view the results, the footer placement is turned off. Then I "right click ... view source" and highlight everything and then copy and paste it into a new document index2.html everything works fine.

That's right, exactly the same code, different results. I do not understand. This is not a live site yet, so if you want to see 2 files in action I can get the urls via email. Just shoot me asking .. always ... and I'll send you 2 page urls.

All other browsers work fine, so Firebug is out of the question :(

This is seriously a markup of the mind .