NOTICE: Our Community is moving. Get more information.
I have the same problem, but the proposed resolution didn't work for me.
I tried it on the server machine (Windows Server 2003 R2 Standard, 32 bit) where CaliberRM 10.1 Update 1 Hotfix 3 (Server and Client) is installed.
My resolution was to change back the orb.properties file inside the bin folder (I still have both versions): there were a few lines that 'stucked' DocFactory2 and after deleting them, DocFactory worked perfectly.
Moreover, after document creation, the certificate has been correctly installed.
Finally, when i did the same process on my laptop (Windows 7 Enterprise 64 bits, CaliberRM Client 11.0 Hotfix 2), I was able again to create the document, but no certificate has been installed in this case.