I had the same issue on ours. Here was the fix, based on past experience with other rack & pinion driven routers:
NOTE: You will probably have to adjust the limit switches to get it to re-home after doing this procedure
1. Home the machine.
2. Loosen the 20 gantry bolts (on our Saturn 2 - not sure how many on the Saturn) to finger tight.
3. Re-home the machine.
4. If the gantry still appears out of square, manually pull the gantry into close proximity on the side that's off. This is where you may have to adjust the limit switches.
5. Jog the gantry around the table 2 - 3 times, then home it again.
6. Snug the bolts on the Y side.
7. Re-home the machine.
8. Snug the rest of the bolts down.
I was having trouble homing our machine after trying to adjust the limit switches to get it to square. After running this routine it homed right away.