ON the Aquamatic pool covers before making any adjustment with the cover closed, walk on the cover at the deep end this will shift the cover material and will most likely fix your issue.
Aquamatic cover systems have an equilizer pully system for the ropes in the center of the vault back wall, look at the top back of the cover in the middle of the vault with a flash light if dark, you will see this pully system. It should be in the middle when closed and will move from one side of or the other to help keep the cover pulling stright. Watch to see what the pully does as you open and close the cover.
I bet that the walking on the cover to release extra material out and reroll correctly will fix your issue.