I decided to upgrade my Maker Select with a glass build plate and have been trying to level it using the paper method for about three days. I've tried moving the head all over and leveling all four corners and the center, but every time I get back to where I started it's no longer level. I pulled out a proper bubble level and noticed that when I move the y axis carriage it seems to warp, presumably because the rods are not straight. Did I break something? Or am I just not doing something you are supposed to do when you install a glass bed?

I'm not sure which information you guys need to help out, but I took some pictures of the difference in leveling from moving the y axis.

Y at origin with level

Y 200 with level