This looks like a joint orientation issue.
Simply put, the joints in your skeleton need to be orientated the same way (or as close as possible) to the mesh you intend to retarget from - there are ways around this; by only using IK-based retargeting and ignoring the rotation of the target bones, however, in your case I'd suggest not working around it by fixing the joint orientation at the source to avoid future complications.

As you can see in the above image, the X-axes of Manny's leg joints are "looking down the chain", where the X+ points at the child's bone or the parent bone depending on the orientation (in this case the orientation is flipped on the left limbs to more easily allow mirrored movement).
I'm unfamiliar with Cinema4D's rigging toolkit but I'd suggest looking for ways to set the orientation of your joins so that X+ points down the chain toward the children or leaf nodes, then flip the orientation from the Left Hip and Clavicle joints.
Note: some DCCs have different coordinate spaces, ie. Cinema may by default orient joints with Z+ points down the chain if this is the case it may be a matter of ensuring a correct unit conversion in the FBX exporter.
Hope it helps.