Here is the known issue list in Ver 4.4. We are in our full power to fix the major problem, meanwhile, in this topic thread, we will also provide ways to workaround:
[Layer Issue]

• Can’t adjust the layer order
• Unexpected Layer Change with applying the Head.

[Character Head Issue]

• The head rotation has no response when using Face Key Editor.

[Character Flip Issue] 

• The motion looks strange when applying “Flip Hip” 
• Character’s position changes when breaking a motion
• The legs or the entire character disappear when applying the motion 
• Jitter effect when two motion clips detaching from each other
• Discrepancies while flipping body with the Constraint Keys on
• Other Flip Issue
• Using "Flip Body" on a character holding an accessory will cause the accessory to change hands.
• The retargeting of the Motion Bones are flipped when the character is flipped, but this does not influence the final result.

[Retargeting Issue]

• The feet of the character jitter after retargeting.

[Photoshop Workflow Issue]

• After applying a 3D motion layer with 3D Motion Convert and lauching to PSD causes the character to reposition.

[After Effects Workflow Issue]

• The Z-Axis failed to transfer to After Effects after having activated 3D Motion Converter's Z-Axis.
• When the "Body Flip" option is activated in Motion Link or 3D Motion Converter for and exported to After Effects, the character has a tendency to lean right when flipped in the side-view. 
• When a key is set on the Z-axis and the character is exported to After Effects, the linked accessories tend to drift away in the side-view.
• When "Flip Root" is performed on linked props and sent to After Effects, only the character is flipped, not the props.

[Others]

•  Under the influence of the Motion Link or 3D Motion Convertor Link, the character floats 7cm off the floor.
• When multiple motion clips contain keyframes, and a motion clip is replaced, all keys of subsequent motion clips will be erased.
• If the hip bone is slanted, when applying 3D motion, with translation and Flip data, the animation will tend to jitter with directional errors.