What I've noticed from using the Instance Maps is that I can select any of them bar Shadow Labs and they'll work. As soon as I select Shadow Labs everything else stops working. Anyone else noticed this?
I'd like to add a little bit to this issue that I haven't seen yet.
This issue seems to be vary a bit, sometimes I can view the instances, other times not. I haven't yet been able to find out when this happens, but I did notice that whenever this manifests, that the "how to use" text in the upper left corner of the map (but not the zone info from another part of Cartographer) will be overlaid by the active map itself (those areas that are also covered by the FoW).
Map notes themselves work normally, as does every other part that I personally have in use, InstanceMaps is shown as active, and no LUA errors appear, so I can't give any of that. The instance maps simply don't show once this bugs (no matter if by clicking them in the list, or the auto-select once you enter that one). Occasionally I noticed that it actually shows the whole outland map, but all the notes themselves are from Zangarmarsh (while in SSC), and if I right click it actually zooms out to what I could see, then I can zoom back in.
Beyond that, I can't add anything else, though if you have ideas I should try out, I'll do that.
Had the same issue yesterday (also kept carto up to date)
What I did to fix was removing carto completely, including the cartographer saved variables and then reinstalled and redid the settings. Most likely it was the saved variables at fault for making Instance Maps not working.
Was no big loss for me at least, since I found a new Cartographer_Data on Wowace files for herbalism and mining, used it for the first time and its pretty decent with no duplicates showing like wowhead's version does!
edit: scratch that, thought I'd check the instance maps again and selecting them does nothing at all again! :(