OK, an update: The overpayment was definitely shown on the IRS website (see the post above; create an account). After waiting several months, I decided to phone the IRS again. It took quite a bit of persistence and many, many hang-up-and-dial-again efforts. Eventually - like an hour later - I spoke to another nice lady at the IRS and she did find the overpayment and that my refund for that was supposed to have been issued way back when I first spoke to them, but for an unknown reason the payment did not process. She re-initiated the process and said a check (or direct deposit) will arrive in 6-8 weeks.
If not for an unknown holdup, I'd have my check already. Of course, mid-October is a BAD DAY for the IRS, so wait a while before trying to get in touch with them. I'm waiting until Thanksgiving and if I don't have my check I'll call them again.
Bottom line: They'll get to it, in their efficient-government way.
