I’m sorry this won’t help like you need: I only export mannequin animations from blender to UE4, Mr. Mannekin Tools automatically exports everything correctly, so it’s definitely a blender/plugin problem.
Are these things you are creating? If so, do some dummy tests with a time-cheap cube and nose character. or a simple animation(slide forward a little), and play around with rotating it/settings and test the export/import process. Trying to figure it out at the front end of a simple dummy project, not with your existing animations, will help you decipher the problem fast, programmer style)
You’ll either find the snag immediately or eventually. Best of Luck and sorry if this unhelpful post aggravates your suffering )= I feel you!