Dreamweaver template files updating, but javascript/jquery not being called on random pages.

Hello,
I have been tasked with updating the navigation on a site that is using a Dreamweaver template (DWT) as the base file. The navigation was originally built using jQuery navigation UI, however this did not address all of our needs and I have updated it with another version of an accordion.
The .dwt file only is only controlling the navigation and the head of the site.
I have integrated the new xhtml structure and added/removed javascript/jquery into the .dwt file. I saved the file, therefore updating all of the relevant .html files, and verified that the accordion works.
However - the accordion does not work for all of the xhtml files. Some files, seemingly at random, are not pulling in the javascript.
When opening the relevant .html files, I can verify that they have all been updated with the new xhtml and the correct javasctipt. However, when viewing the .html files that are not displaying correctly with FireBug, I can see that none of the jquery/javascript is being applied to the navigation (classes are missing that are injected into the xhtml, but the structure and css is correct).
I've done some research and the only issues I've been able to find are related to .xhtml files not being updated with the correct code, but in my case all of the affected files have the correct xhtml and scripts in the head.
Does anyone have any light to shed on this subject? I am quite puzzled.

While I understand that looking at code is the ultimate way to find a solution, the intent of my question was not "how do i fix this" or "what is wrong with my code" but rather "does anyone have any idea as to why this would be happening". Or even, "where would you start to troubleshoot this".
I made my question general as such because I intended on trying to troubleshoot on my own in order to better understand the issue.
Thank you for stating the obvious, not all first time forum posters are completely unaware of how to ask questions properly.

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