It sounds like your machine was either screwed up from day one or something happened to torque it. Did a semi crash through your shop lately?
I believe you can adjust the squareness (which is probably the issue) of your gantry by loosening the large bolts holding the cross member to the end pieces. You'll probably have to do it on both sides of the gantry to get enough adjustment. Once you have the wheels in the track, you'll need to check the squareness of the spindle or router to the table before tightening the bolts again. These bolts need to be torqued to the right setting so I suggest calling SB and ask them what that is.
ShopBot Details:
2013 PRS 96x60x12 (Centroid upgrade)
4hp Spindle
12" indexer
Aspire
Rhino
Fusion 360
Ferrari 360
Prusa MK3S+
Prusa XL multi-tool