If you used the print option>save as PDF, it seems strange because this pdf making is handled by the system, not by Word. If you did it through Acrobat/Reader plugin, it may be prone to all sorts of things up to incomplete file conversion. Another thing to look for would be protection. If each PDF is protected, Acrobat cannot merge the files. If this is the case, revert to generating PDF files through print option or get a program called PDF protect that can either protect PDF files or deprotect them.
After making PDF versions of Word 2011 files, I found that I couldn't merge them to one file in Acrobat 9.0. Acrobat 9 becomes unresponsive.
This occurs on two different hardware platforms, a MacMini and a MacBook Pro.
Reverting back to Word 2008 eliminates the problem.
Anybody else see this kind of issue with Word 2011 and Acrobat 9?

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