It does sound like the rear wheel is not aligned with the front or it is cocked at an angle to the vertical plane of the bike. Both are quite possible on a Commando.
Do as suggested above and check if the front wheel is centred in the forks, then check, with two straight edges, if the rear wheel is in line.
With the bike off the stand, grab the end of the rear wheel and pull hard from side to side. This should show if there is play between the engine/gearbox/swinging arm and the frame. If there is play, it won't show up with the bike on the centre stand.
When I removed the rear mudguard on mine, only then could I see clearly that the rear wheel was cocked from the vertical (because the swinging arm was bent). And both wheels were offset to the right of the centre line of the bike.