Enable for commenting in Reader -- Inconsistent behavior?

Question

Many similar threads on the forum, but my problem seems different.  I've built a portfolio in Acrobat Pro 9, containing multiple folders -- each with multiple files.  I want to enable all the files (mostly pdf's) for commenting in Reader  (urging clients to upgrade to Reader 9).  The portfolio will have password security allowing printing, commenting, forms, and existing signatures.
With security off in Acrobat Pro, I opened each folder, selected all files as a group, and enabled for comments under the comment menu.  (Although that menu item is followed by an ellipsis ...., no dialog box followed.)  Still in Acrobat, I confirmed that the Comment and Markup Tools were available for each file.  I then reset to Password Security under Portfolio Properties, with permissions as noted above, including commenting.  Immediately after this, I saved the portfolio, and the title bar changed to SECURED as expected.  Still in Acrobat Pro, I checked all the files in all the folders, and the markup tools remained available  (except with jpg files, as I think is expected).
When I open the document in Reader 9, only the first file in each folder has the Comment and Markup Tools menu option available.  I repeated the process described in the previous paragraph, this time enabling each file individually then setting the security for the portfolio.  This managed to get two more files with Comment and Markup tools available, but the remaining 20 or so files still had none.  When I open Portfolio Properties in Reader 9, under the Security tab, the upper box shows Password Security and the Show Details button pops up confirmation of the permissions I had set, including that Commenting is allowed.  However, the lower box, Document Restrictions Summary, gives similar information, except that commenting is not allowed.  This discrepancy makes no sense to me.
When I open the Security | Show Security Properties ... for an individual file, Commenting, Assembly, Signing and Template Creation are starred as restricted.  For the few files that do allow commenting, the starred fields are the same, except that Commenting is unstarred (allowed) and Form Fields is starred instead.  All the files were set up the same, and most are pdf's created from Word or Excel.
Any ideas what is going on and how to fix it?
Thanks for the help.

Answer 1

OK, I think that is best suited to larger organisations who create lots of documents that need to be commented on around the organisation.  Our application is a CAD system that exports a surface based CAD model as a U3D file embedded in a PDF.  So the user in the CAD Office creates a CAD model and exports a PDF as a lightweight file format to pass to someone in another department, or maybe their customer.  They want to be able to measure the odd length and hole diameter easily in Reader.  I've been asked if the CAD system can create the PDF file already enabled for commenting.