First, unparent your mesh to the skeleton (or this may cause crashing later when importing) alt+p, clear parent.
Now, go and create a root bone if you do not already have one you want to use as root.
Join all your bones together into one armature by selecting them all in object mode and pressing ctrl+j.
Select the armature and go to (usually tab)edit mode, select all the bones that you ARE NOT your root bone, then finally select the root bone and press ctrl+p (make parent), and select keep offset, (assuming you dont want to move your other bones onto the root bone).
Export the armature as fbx as you where and it should work now.