Reversed brackets in Arabic extracted text

I'm working on a system that is reasonably good at extracting text from two different PDF documents and comparing them. It's built using PDFL (I'm hoping the community for Acrobat SDK will be willing to help me out since I can't find a forum for PDFL.)
I run into a problem when working with Arabic text. The issue is reversible symbols like brackets ( ( ), { }, etc) and some other things (like < >) are visibly identical in the two documents, but are encoded as their opposites.
i.e.
Document 1 - Text looks like (ABCDE) and is encoded with the unicode values for (ABCDE)
Document 2 - Text looks like (ABCDE) and is encoded with the unicode values for )ABCDE(
I figure this has something to do with right-to-left read order and mixed font detection or perhaps some other font-setting.
I need a way of detecting when this reversal happens so I can compensate for it when extracting the text. I'm stumbling in the dark at this point and would appreciate any direction that could be given.
Thanks,
NN

I can't actually post the PDF (confidentiality agreement prevents it), but I can give you some info:
Document 1: (where encoding is correct)
Created by easyPDF SDK and uses SimplifiedArabic font family for the problem characters and their surrounding text.
Using the Acrobat TextSelection tool to copy/paste the problem text from this document into Notepad results in text that looks right.
Document 2: (where encoding is reverse of displayed character)
It was generated by InDesign CS3 and is using the WinSoft Pro font family for the problem characters and their surrounding text.
Using the Acrobat TextSelection tool to copy/paste the problem text from this document into Notepad results in text with brackets reversed.
What should I be looking for to be missing/wrong from the font definition or content stream?

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