Missing Commenting Toolbar for Acrobat Reader 9.3

Our company's standard desktop PCs run Acrobat 9.3.4 , Windows XP SPII (still), and IE 8.0
I have 2 PDF files, with the same Reader Extensions applied to both (commenting). The source of the PDF files was from Autocad (plant drawings). They are produced in exactly the same fashion , and in fact were generated within minutes of each other using an automated process.
What I am trying to say is that , from a PDF data structure point of view, these files are the same.
The PDF files are put on a web browser and users can access and open them in Internet Explorer within our intranet.
I know that Reader Extensions works for both because when these PDFs are opened up on user's desktop PC that only has Acrobat Reader in Internet Explorer we dynamically add annotations (using the Javascript API) to the PDF file as well as support other Reader Extension features such as spawning templates.
Here is the problem.
One PDF file has the commenting and markup toolbar when opened.
The other PDF file does not.
And when I right click on the one that does not Commenting and Markup is NOT an option. I cannot find a way to enable this.
This is now a major problem for us as we would like to support adding comments to these PDF files.
I cannot fathom what the difference is that would trigger Acrobat to suppress/ show the toolbar for one file and not the other.
So I have 2 questions.
1. What stops Acrobat from showing the commenting toolbar?
2. Is there some way through the Javascript API that I can force the commenting toolbar on for the PDF file that does not have it?
Your help would be greatly appreciated.

We have found an answer.
I still do not know why there is inconsistent behaviour, but if we execute the following Javascript (we are putting it in the /After section), it enables commenting
Collab.showAnnotToolsWhenNoCollab = true

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