When I changed the second icon (added .pdf as only .PDF was in the 'filename patterns')the pdf symbol on the first icon disappeared again to be replaced by the blank icon.
Remember, linux is CasE SensitivE
So the extension .pdf is not going to be recognised if the filename pattern is set to *.PDF
R-click a pdf file
Click the wrench
You should see both *.pdf and *.PDF listed under "filename patterns", if not click ADD and add the missing one(s)
Check the Application Preference order has your preferred viewer at the top of the list, if not, select (or add then select) it and move it up to the top.
Click the Embedding tab
Make sure "Show file in separate viewer" is selected.
Also remember that linux is smart enough to know a pdf file when it meets one - so, unlike windows, you don't really need the pdf extension at all.