I have had similar problem. And I too, have spent endless hours trying to correct. At first, I panicked & started deleting people as I am only interested in my DIRECT line.
Disconnecting doesn't work, deleting a person and then re-adding the person & connecting them back in doesn't work. I can't wait to have a FIX - I love my Ancestry.com but I think for what I pay each month, I should be able to have the "relationship" correct. If someone comes up with a fix, I want to know. Actually, I think Ancestry.com should have program that they can run - or let us run to correct.