Transmission replaced under warranty but charged for TCM

We are the original owners of a 2000 Sonata GLS. At 69,906 miles, the transmission failed (no reverse and would drop into neutral at 60 MPH) and was replaced by a dealer, under warranty. This was in May '06. In Jul '06 at 71,273 miles, a "check engine light" came on and the tranmission felt like it started out in too high a gear. Back to the dealer, who told us the "transmission control module 95440-39014" and "bank 1 sensor 1 oxygen sensor 39210-3712A" needed to be replaced. We were charged for these parts ($658.69 for TCM and $48.40 for oxygen sensor) and labor to install them. My question is: should the TCM have been covered under warranty when the transmission was replaced? Wouldn't the TCM be considered part of a transmission replacement if it had to be done within 1365 miles of the replacement? Just concerned, as the transmission was just replaced (again!) Under warranty. This time because there was a leak that couldn't be fixed. The dealer says the TCM is not a warranty item. To their credit, they loaned us a car to drive while the Sonata was in their shop, but I need to know if I should pursue reimbursement from Hyundai's National Consumer Assistance Center for the previous TCM replacement. Thanks for your advice!