Well, Reader doesn't convert Word docs to PDF. Sounds like you are using the Microsoft PDF converter so I'd check in their forums first
(if they have any that is).
To convert to a PDF document, I save my Word document as a PDF file. The logo looks like Adobe, but you think it is actually a Microsoft converter. Is there an Adobe product that converts Word files to PDF? Maybe it would work better..
Your system supplies the logo when it associates files. When it sees PDF, it assumes you want to use whatever PDF viewer/Editor that you have installed. In this case Adobe Reader. It doesn't necessarily mean that it's an Adobe created PDF (in this case, it's not).
Adobe Acrobat is the product used to create PDF's. Adobe Acrobat is the only PDF creator that creates ISO standard PDF's that I'm aware of. If you use the convert function, it will also keep all of your links and various other interactive items intact.