Rear tyre not seating on rim

[slappy]

With the tyre off, check for any damage to the rim. It is possible also the the rim is out round or has a flat spot, a friend had similiar trouble and I took the wheel into where I work and using a dti clock found two large flat spots, he had to buy a used wheel in the end.
Where the bead sits get some emery cloth on it as well and lightly rub it down, this will remove small imperfections and also help to show up any dings or dents.