If you register with one board and another is warped, it can throw off the reg. In addition though, check the flatness or plane of the screens themselves.
Screens can easily get out of plane.
When everything is working right, the boards should be in perfect plane with the screens. All four corners of each screen should be exactly the same distance from the platen. If they are not, it is worth the time and effort to fix them. Warped boards should be replaced. Most often, boards are warped by excessive heat.