Thanks Jason I didnt want to jump the gun.
Right looks like its very simple to fix I have done a few tests and all seems to be working prefect so far (fingers crossed).
1. Outside Dreamweaver rename Fuel.php.js to fuelphp.js
2. Inside dreamweaver do a find/replace on all local files (7 instances should be found)
replace with fuelphp.js
Upload the changed files and test
I have found it works in all browsers with colour highlighting and the correct link now shown in dev notes.
I hope this helps some of you who are stuck too.
Just to add a note to this:
A slighltly quicker route is to rename Fuel.php.js from within Dreamweaver to Fuelphp.js and Dreamweaver will prompt to update links if you allow this Dreamweaver will successfully update all instances with no issues.
Hope this helps.