This actually rarely happens, but I've had a two cases in the last three years where a mesh fully broken up and named correctly will not bake when matching by mesh name _low _high. Today was the second time this has happened and consists of a bit more than fifty parts.
I had to explode the mesh to get the correct bake as the prior result would be 100% identical to not using the feature all together.
Unfortunately I cannot provide the meshes that do this due to them being someone else's IP, however I thought to see if anyone else by chance has experienced this rare occurrence? If I can duplicate it with a random mesh I'll post back, but who knows when it will occur again.
As an added note, I bake by mesh name all the time without a problem...