Okay, false alarm. After cleaning up weird mod versions for a neater bug report, the problem went away.
In case you have a morbid curiousity about weird installs - at one point I let Steam auto-upgrade to 1.3.x, ran CKAN, and then realized I should downgrade to 1.2.2 so I'd have my mods available. Anyway, several mods were left at versions that supported 1.3.x but were incompatible with 1.2.2, including ModuleManager, and CKAN will not downgrade packages through the GUI, only when run at the command line. Other mods were also broken-ish, but ModuleManager seems the scariest and the most likely to have caused bugs.