Hi,
If you have used upload and download feature of WD then it will convert the PDF into XSTRING. now when you try to download the same then you might need to convert it back.
But if you are again using same DOWNLOAD feature of WD then it will automatically detect the XSTRING and converts it.
From the statement you have made it seems that conversion which WD performs during download is going wrong. You need to check on the Adobe services which are running on the system and also try to check the latest SAP note for your upgrade to support PDF files on EHP6.
Regards,
Praveen