Searchability & metadata extraction on password protected or compressed PDFs

Hello,
I am currently putting together a new document management system at my company (using http://www.alfresco.com )
and part of the functionality will involve automatic metadata extraction from stored PDFs, and google-like full-text search of PDFs.
We seem to be running into a few problems though -
All our PDFs were password protected in Acrobat to have a "read only" security permission - yet this seems to be blocking the metadata extractor.
I wasn't expecting this - obviously, Adobe Reader can still read the metadata, I'm wondering does it do anything special that other clients aren't allowed to?
Also, I'm wondering if the "object level compression" and "compress text and line art" Distiller settings could interfere with PDF content/metadata readability?

Let me expand a bit on Aandi's comments...
First, PDF document support two types of metadata. "Classic" metadata (called Document Info) which is stored in native PDF data structures and will be encrypted when the rest of the document is, so that you can NOT extract the data w/o processing the file as a native PDF document (instead of as "raw data"). "Modern" metadata is stored in a PDF in an industry standard XML grammar called XMP and will be left in "plaintext" when the rest of the document is encrypted - so that it can be located and extracted w/o the need to process the PDF natively - though it is still recommended!
Second, as Aandi points out, "compress text and line art" has been a feature of PDF since day 1, while object compression is newer feature of PDF introduced with Acrobat 5 (about 7 years ago!). NEITHER of these features will effect the "Modern" metadata, since it is required to always be in "plaintext", HOWEVEr, the latter CAN effect "Classic" metadata. Another reason you need to process a PDF natively.
Hope that helps...
Leonard

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