S and T should have little to no effect on a 4-axis palletizer robot, however. Hmmm....
One quick check you can do: Try moving the robot to those points using LIN, rather than PTP. LIN commands essentially ignore the S and T variables in favor of maintaining path interpolation. If A6 still behaves incorrectly, then the issue is probably in the position data, or possibly something has gone wrong with the re-teaching of the Base frame.
Another quick check: send the robot to a defined position in the Base of your palletizer program, using something like PTP {X 0,Y 0,Z 100}. That should put the active TCP 100mm directly above the original point of the Base. Try this for a few points you can easily check against the physical Base -- this will allow you to confirm if the Base is taught correctly. Leaving out ABC values will eliminate them as a possible factor.