Yep, I can remember this about four years ago when I was booking one of those round Australia trips Same deal, the agent could see different availability to what I could see and I was online beside the computer at the same time. In the end it didn't cause any problems, in fact the agent got me onto an intl. leg that I couldn't even see for one part of the trip.

You'd think in this day and age it would be sorted though, it makes the whole process look a bit hit and miss