I selected the Bloodbath scenario that’s on the online challenge list, and had a blast playing it, but later noticed that both alliance and imperial factions were unselectable. I did some investigation and discovered that the auto-downloaded scenario got added to the game list in the data files, despite it being unavailable in the offline single-player mode, and thus the game concluded that I hadn’t beaten all the scenarios (and thus denied me the unlock races).
Makes no difference at all to the stock game, but if modded scenarios become significant then this needs fixing. This is particularly significant because I didn’t download anything external to the game - I just selected a non-standard challenge scenario from the online challenge list. Players could easily stumble into this and not know how to fix their data files.