Solved. Thanks for checking!
OK, this was useless. How about posting the solution for those in the same situation? 
bummer. I’m having the same issue, but instead of finding an answer I find the question deleted.
Edit:
I determined what was causing this. I had a plane above my terrain that I was using for scrolling clouds. The plane was set to not cast shadows (and it wasn’t casting them on the terrain). I had my sky light turned off as well (and only a directional light). But the trees (and only the trees) were still being shadowed by the non-shadowcasting plane. Turning off the cloud plane while baking lightmaps solved the problem. Seems like an obscure bug in the lightmapping process. Turning the cloud plane back on after lightmapping set things back to normal.