is it a standard gearbox or has it had a limited slip diff added or anything else at any point?
They can sometimes turn in the same direction, can you hold one of them still with one hand and turn the other with the other hand?
I guess if you think it's the gearbox still, you can open it up easily once it's off the car (it's just a load of 10mm head bolts you can see on from the bellhousing side), then have a look at the diff. It just lifts straight out once you separate the casing.