Geesh, after sifting through many pages of different searches in Bing, I FINALLY found the problem! I'll post it here in case anyone else runs into this: Go to Tools>Options... Then click the Print tab and UNCHECK "Field Codes".
This is very generaic issue that chang the flow of document while converting MS Doc to PDF. After googing and testing different software I found a PDF Converter, that converts 100% fine copy of Doc to PDF. Watch the below tutorial to know how it works.
It is also featured on CNET free downloads here.