PDF is an output format not a data exchange format. So you will get now and then problems like that. What you could try: Do not copy/paste content from PDF (via Acrobat) use the export command to save an RTF or Word file.
Exporting as rtf or doc from Acrobat turns out worse results than just copying it from Acrobat Reader. Exporting as txt from either Acrobat or Reader gives a file filled with full-stops rather than any text.
And yes, while I do realize PDF was mainly intended for printing, it has become one of the biggest formats for data exchange. It is even a standard e-book format. And these requirements had to be fulfilled, why else do the ToUnicode and other hacks exist?problem
Also I'm still not sure if the problem is with inDesign or just the PDF readers not implementing things correctly because I get wildly different output text from different readers.
Any more ideas, please?