It really sounds like you tweaked something as the arm and dish are very sensitive to being moved by outside forces.
You could stow the antenna and then when the LNB is 1-2 feet off the roof measure from the roof to each side of the bottom of the LNB. They should be the same distance. You can also look to the dish itself and see if there is even the slightest wrinkle (bend, scratch, wave) anywhere. The arm of the LNB being slightly out of line would be my first guess / best guess so you also might want to have someone watch the signal and try gently twisting the LNB to see if 99 appears.