p38 2.5 diesel gear box issue

Righto.. we have a P38 2.5 diesel..(fellas car). that needed a gearbox.. (would only drive in first then 3rd, not in drive) so we got a donor car (exact same engine) and the fella switched the gear boxes over .. the car will now drive like it should, selects all gears etc and works BUT power is down in comparison to our other p38..it doesnt seem to be moving into the gears as it should and revving high. Does the new gear box have to be programmed to the car??? could anyone give us some tips..
Although today the p38 i use has also started to gear change strangely and seems like its in limp mode..:/ No warnings on dash etc