I am experiencing the same issues Anthony had in the original post. Similarly I have no issues when using gnome-shell on my Thinkpad's display however when plugged into the Ultradock and using an external monitor I have the exact same symptoms.
Workspaces 1 and 2 initially available however appear to be mirroring each other. When you try to use Workspace 2 it collapses and you are left with the one Workspace and are unable to open additional. I upgraded to gnome-shell 3.12.2-3 from unstable this morning and unlike Anthony upgrading to gnome-control-centre 3.12.1-4 also has not solved this one for me. If you would like contents of logs etc... please let me know. Regards Harry
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