I have found a solution to this problem.
If you put the javascript in Page.php or on the template page.ss, SS will load the script on every page everytime, even when you do not require it to be loaded for certain pages.
The solution is to modify cms/javascript/tinymce.template.js and a line in:
valid_elements : (near line 43)
to allow <script> in your TinyMCE HTML
For more detail please check out this link:
http://wiki.moxiecode.com/index.php/TinyMCE:Configuration/valid_elements
This way, I can include the <script> to the HTML, to only the page I want.
I still do not understand this warning message in Firefox error console:
Warning: Error in parsing value for property 'filter'. Declaration dropped.
Source File: http://www.kudesign.co.nz/studio/
Line: 0
Any tip will be much appreciated!!