This is unfortunately an issue of Lotus Notes. One workaround is to save the PDF to the global inbox (~/Library/Application Support/DEVONthink Pro 2/Inbox), another one is to add an alias of DEVONthink Pro (Office) to ~/Library/PDF Services and to print to this alias instead.
Yes, Global Inbox is what I end up using for the moment.
I think this one is not going to work, if you already have DTP up and running as it’ll complain about databases being opened and in use already by that copy of DTP.