Collapse and inability to compose correctly

My problem seems to have started after I used the rotary tool. After doing some engraving on a glass I switch to another project cutting and engraving. I discovered that my y and x axes were not accurate, so I calibrated the X axis, which went fine but I never could properly calibrate the Y axis. I read that it may be because I had to close down all functions related to the rotary tool. So, I checked everything and closed down all rotary functions. Now when I frame, it crashes into the walls, and now it frames bigger than it should be and is not even framing where the drawing is located in Lightburn. I loaded the pref backup to a date that I did not have any problems and still with the same problem. All these test were made on a new window. At times when framing is completed it does not go back to home. I am using this machine for a year now and never had this problem and I always used Absolute Coordinates.