You are writing what you are thinking, and its sounds illogical.
So when you push the Baja forward one wheel spins forward, and the other one backwards?
I think that what you are saying is that when you have the rear wheels in the air, and push (by hand) one of the wheels, the other wheel spins backwards. If that is the case, it is normal to a certain point, it means the brakes are dragging. On yours may be spinning the other wheel the opposite direction because the oil is too thin and the brakes locked in neutral. On mine, with 20K diff oil, brakes clear, when I lift the baja (engine not running), and I spin one of the rear wheels, it spins on the diff shaft and you can see the brake rotor spinning, and the opposite wheel not moving, but if I engage the brakes, the other wheel spins the opposite direction. It is a open differential, not locked, and thats they way it has to be for better turn radius and prevent any binding on the transmission.
Several things; throttle servo end points not set correctly, the brake arm linkage not set correctly. Please view the pdf link, HPI Baja 5B, it is not the same RC, but gives you an idea of how to set your controller and dune runner adjustments. I recommend read the complete manual for a full review and refresher.
https://www.manualslib.com/manual/454166/Hpi-Racing-Baja-5b-Rtr.html#manual
And looking at the pictures this is the manual that is as close to what you got;
http://www.redcatracing.com/Rampage-DR-4X4
View the download manuals
**On some clutches, the spacers located on each clutch shoe are too thick, and the bolt sides are rusted or too rough. Smooth out all surfaces with 400 or so sandpaper and water, and if need be go to Lowes or Ace Hardware and getting thinner spacers. The shoes installed (without the spring) shall move freely. Sometimes if there is some binding and too tight, they will stay stuck open once they heat up, it has happened to me. These things are assembled a dime a dozen, and QC is dramatic from one clutch to the next, and that goes for all other parts.