Not per-say. after the tune your car will run a little harder so it shows the faults in the system, hence why most people need to upgrade right at the tune.
So you moved the coil pack from 3 to another and got the same misfires still in 3? If so we can tell its something to cylinder 3. So have you changed the spark plug in 3 also?
I would double check the coil pack method and then change the plugs (they aren't to expensive so its no biggie) then you may want to go on to a shop after those if still issues to see what else could possible be wrong with cylinder 3