Hey IndyJo,
I have been doing some retargeting skeletons myself and it very tedious to get right - especially using skeletons that don’t exactly match the UE4 skeleton.
My best guess for the problem is that the pose of the skeleton is not in the exact pose of the UE4 skeleton pose.
Another issue I have found is that if your skeleton is missing bones or the bone structure is not the same. I have a lot frustration with this myself and hope you get it working. In my experience I try to use the UE4 skeleton whenever I can.