Well , I have found a bug reported for this problem, happening to other´s files extension. I have updated bug track reporting that PDF files are also affected.
They are working to fix this for next version.
This information might be useful:
I could not reproduce this with Desktop 9.10.0.554 on a Windows XP SP3 connected to a Windows Server 2008 SP1 and SP2.
All files/folders accessed via UNC can be encrypted/decrypted fine using NetShare and even the overlay icons were fine.
Please, try mapping the drive and access the file.
If doesnt work , you can try using 9.10.
Good luck