This may not be applicable to your situation, and maybe this has already been discussed elsewhere, but I discovered last weekend that RR seem to book out of the Internet and Discount Fare buckets. Or at least that was the case for me...

My reasoning is that my friend (who was using a RR) and I (who was just booking a regular trip) were purchasing a round-trip from HOU to LAS, and the flight we wanted had RR availability for her and Discount Fares for me. She used the RR, and poof, my Discount Fare ticket was no longer available! Considering we were at two separate computers and were purchasing the tickets at the exact same time (her just slightly before me), I can only suspect those are the buckets RRs use for availability. Maybe its not, but it sure seemed odd to me...