After exporting my rigged mesh as FBX, the bone structure changes:
Most of the info is in the image above. I had problems with retargeted animation on upper part of this character in Unreal Engine 4. Then i have noticed that 'head' bone is missing (actually, the neck bone is now named 'head'). I have checked my mesh in 3dsMax, to be sure that problem is not on Unreal Engine side.
I've tried exporting it with ASCII version of fbx, but result is the same. It looks like it creates root bone out of 'hips' bone and 'collapses' all other bones in root direction. I've also tried to create root bone manually and parented all other bones to it, but with no success - bone structure is still altered in the same way after export.