How different is 'different'? If they were within 5-10% (depending on mesh) then it may just be an artefact of the way analysis works normally.
I'd give a highly qualified 'yes' to your question of driving by one and dividing that force by 2. However the stress will be different since you end up applying twice the force on one side.
Motion analysis, since it is rigid body, has issues with redundancies. A symmetric system like you've shown will be statically indeterminate so it is common to see unpredictable force readings.
One workflow is to analyze half the system with half the load as you have discovered (as long as it is an acceptable assumption for the geometry)
Another workflow would be to try to eliminate the redundancies. In your case I would define flexible "bushings" on the mates for any of the redundant components. This is done by editing the mates and going to the Analysis tab while Motion analysis is loaded.
Once you put in some bushing stiffness the system should be solvable, even as a full model.