Let me ask a few, very basic, questions. Gpredict is written for Linux, your computers are both running Linux? The only reason that you would show different positions is that your TLEs are not the same for both computers. You updated TLEs (this is what we expect that you would have done) for both?
I am not sure why the two computers would show different positions but you could schedule to listen to a few satellites and see which one is more accurate. That really should not be necessary but it would tell you which is correct.