I'm using Word 2007SP2 and Acrobat 9. After pasting ChemDraw structure into Word, I choose Save As, and then choose Adobe PDF. There is no structure in the PDF.
This problem does not occur with version 8.1.2 of Adobe Acrobat or if you use Print to PDF rather than Save As PDF.
We have confirmed that the Microsoft patch located here:
does work, HOWEVER, you must choose Save As from Word and then choose the "PDF or XPS" option. This option is present if you have MS Office 2007 SP2 installed.
If you have Acrobat 9 installed, which installs a Word Add-In, we found that using the Acrobat 9 Add-In from Word to create the PDF still shows a problem. Please note that if you have Acrobat installed, it may install a "Adobe PDF" option in the Save As list. This will not work either. You must use the Save As-> PDF or XPS option to take advantage of the Microsoft hotfix.