In a bizarre inversion of this problem, I installed v1.36 and the graphics submod, and whenever I loaded a game it couldn't find any of the skyboxes. I figured I'd use snuggydoodle's advice of mucking with the module.ini, but when I opened it up, it was already set to loading native skyboxes (LOAD_RESOURCE instead of LOAD_MOD_RESOURCE).
I switched it to load mod resource, and now it works fine. Just figured I'd post this incase anybody else runs into the same problem.
(This doesn't strike me as a bug, per se, so I'm posting it here instead of the bug thread. Should I?)