Build and Run is consitently baking lightmaps incorrectly

Take a look at this Imgur album of the problem:

http://imgur.com/a/bOstb

Basically, the lightmaps are baking perfectly in the editor, leaving me with a lovely scene that's as it should be.

Then comes time to build and run, and when I do, as soon as the build is complete, in the scene, now the lightmap file size and numbers are incorrect, and everything in the scene is baked as pure black and pure white.

Then, when the editor is back in control, it immediately redoes the bake and everything is fine, but not for the builds! Only in the editor!

And if I get it all baked perfectly and then rebuild the game again without "Auto" ticked on that scene, I'm left with 0 lightmaps and all realtime GI.

I tried "Clear Baked Data" and erasing the Gi cache is not an option as this will push back my production schedule by weeks.

Thanks!