I posted this in the bugs section, but I thought I'd put it here as well. Hoping someone who knows what's going on will be more likely to see it.
I decided to change around some of the cliffs on my map. When I play it, the map gets revealed according to where the caves were instead of where they are. Unit pathing works as it should, it's just visibility. This is the area in the terrain editor: (thumbnails are links to big image)
And this is what it looks like in-game:
The blue lines are my best guess at where the cliffs should be. The blacked-out area is where the cliffs were before the change. In the minimap I've circled in red a section of high-ground that gets revealed as if it were on the same level (which it was before the change).
I haven't done anything with the visibility/pathing layers, this is a new map I've only been working on for a few days.
One more thing, I don't know if it's related but when I'm in-game, this map makes the fans on my graphics card spin up faster than I've ever heard them. I have other custom maps with 100x as many doodads, and no problems.
EDIT: I don't know what I did, but it's working now. Just as mysteriously as this problem showed up, it's now gone.