That might be the problem (as you seem to suspect).
Make sure you have the Bubble local media server disabled; it may well be that your clients are seeing the Twonky Server and the Bubble server, and offering you both copies, using certain of the DLNA ‘views’.
Bubble settings:
Settings/Local Media Server/Enable
Make sure this is unticked to stop it revealing its media server to external clients.
I’d suggest the /etc/contentdir mod is the more effective, or less intrusive to the system.
I’ve modified the MyCloud startup script to pull a copy of this from a folder in a share, so that it all starts up tidily. I shut down Twonky first, then copy the files across, then restart Twonky, all in the startup script.
You shouldn’t need to add ‘Photos’ to the media types to make artwork visible in DLNA music players. Only select pictures if you want to be able to browse artwork as a distinct collection, using the Photos or Picture browser of DLNA clients.