If I were to make a guess, I would say the ArcGIS connector is looking for an "ArcGIS Location" field in the lists on whatever SharePoint site it's searching on... as it can't find one, it thinks there are no spatially enabled lists...
I'm not sure if you would be able to create a ArcGIS Location field on a business data connectivity based table though - it seems unlikely... but I haven't tried... 🙂