We are self administering a 401a and just processed first loan. Our question is about the interest that is paid back by the employee. When the money is finally paid out at retirement or termination, how is the interest payback handled on the 1099-R since it is being paid back with after-tax money? Seems like it may be double-taxed?

You would treat it as a regular distribution. That is one of the disadvantages of a participant taking a loan.