I’m also interested. I have the T1 Pro (new) cube set up and have the same problems.
Face 2 and 5 as well as 3 and 6 are mixed up.
Notably, they don’t do this all the time, but often enough. I didn’t use the knock action, so I can knock to get the face update in.
I’d really like to use this cube as central living rool portable control (and also, in a different automation, as pen&paper scene controller for music and lighting). Would be great if it just worked as one should expect it to. 
Sidethought: How do I even find out, if it reports the correct or the incorrect face first? Can I get the raw zigbee data somehow? I am only looking at the helper input at the moment…
edit: Nevermind, I just used rvaidya’s blueprint and it works without problem. No mixed up sides. What I saw with a blueprint that works is: The first face recognized with the faulty one is the correct one, and the updated face is the wrong one.
This blueprint is definately working with my T1 Pro magic cube. ZHA - Aqara Magic Cube (69 actions)