I'm having the same problem with an Carefree SOK II. I think if I can get the fabric centered on the tube and all the aluminum lined up at the top, it will stay in position, but right now the fabric has slipped a bit in the aluminum and that seems to make it wind cock-eyed. After a few in/out cycles, the metal moves enough to interfere with the roll-up. I'm still playing with it, but think I am going to have to remove the topper altogether, get everything aligned right, and then re-install.
2004 American Tradition; 2014 Buick LaCRosse
Homebase in the Ocala Nat'l Forest near Ocala, FL