Inside your anim instance class defaults, Ensure automap target is HAND RIGHT for your case. Also below that section is a structure called mapped bone list open it up you can see Pre-base rotation and offset transform, these will apply to the entire mapped bone list. Pre-base rotation will apply rotation before your values (akin to changing the basis of your input) where as offset transform applies after your input has been fed. If you’re moving your hand/fingers and they bend in a wrong axis e.g. they yaw when they should pitch, you will need to adjust the pre-base rotation, typically in some combination of 90 degrees. These will typically be different for each hand if your mesh is rigged like animators typically do with positive rotation closing your fist. In the low poly hands it uses a pre base of -90 for left and 90,0 180 for right.
That said it looks like your thumb might be in a different space than the rest of your hand and you may need to remove it from the auto mapping list and feed the rigging directly, or go back and adjust your model in your software. If it’s just a fixed offset difference however, you can just add a standard Transform (Modify) Bone node and adjust the offset there after the Modify Mapped Bones node.
If the auto-rigging is giving you a problem, checkout the discussion here for basic details on direct rigging:
https://.com/leapmotion/LeapUnreal/issues/35
Regarding the flipping, it might be occurring due to hand chirality detection, might need a video of the issue to know more.