I had the exact same problem. I made a skeleton mesh in blender with armature. When I exported and imported to UE4, I got a multiple root error. I went back in blender and noticed that my IK and pole targets were not under the Root hierarchy. I selected the IK and pole targets, then selected the root bone, Ctrl-p offset. This made the root bone the parent of IK and Pole-targets. Then I went and unchecked inherit location, rotation, transformation, and connected on IKs and Pole Targets, so it didn’t mess everything up. Re-exported to UE4 and works just fine.
I did all this in edit mode and didn’t have to clear parents or join anything. When you make the IK and pole targets, you have to clear the parents on them to work correctly, but after that you have to re-parent them to the root as I stated above, or UE4 will think its another Root Bone.
Thanks for your help, , you got me on the right track. 