Upgrade to 3.6 from 2.x breaks book serving

Hi,
My world was good with my old 2.x version of Calibre. I added my new books, put them in virtual libraries, tagged them and then connected to the Calibre server with an iPad running Aldiko. I could see my tags and virtual libraries and was able to find my books by tags and the virtual library they were in.
Yesterday I realized how far behind I was with my version of Calibre and updated to 3.6 - and had problems getting new books on my iPad.
I found the /opds after the server URL and at least my Catalog display in Aldiko did not crash anymore and I could get my books from the server.
But I don't see an option to select virtual libraries any longer and when I display my books by tag I only see 30 tags and my tag 'new' is number 50 (or so) and I can't select it.
Is there a solution to this:
- a way to show virtual libraries and
- to show all tags (this might be a limitation of Aldiko, but it does that on iOS and Android)

Thanks for any help you could give me.
Cheers,
Merlin