This may apply to other airlines as well.
We booked Adelaide to Perth to Bali and back last October for our January trip. On way back schedule showed 1hour 55min changeover from International to domestic. I thought this was fine. Got flight out on time, all seemed well. Got to Perth domestic terminal was told our Adelaide flight has already left. Got a 20 minute harangue from the check in girl that our travel agent had broken the rules by giving us only 1 hour to make the connection. I showed her our printed schedule but she just said thats wrong, your travel agent didn't book it properly. We would be waitlisted for the next flight (3 hours later). Told QANTAS would be within their right to charge us extra but they "probably" would forgo this etc.
After about 45 minutes sleep i was not happy with this and asked to speak to the terminal manager. His reaction was very different. Western Australia had opted for daylight saving for the first time in December 06, thus our flight was one hour "late" in arriving. He confirmed our ongoing flight and paid for a meal for us. But he did say that QANTAS had emailed us and showed us the record. OK but the email address was incorrect, which he seemed doubtful about. As neither we or our Travel agent had provided an address to QANTAS this seemed odd.
Overall, if you booked travel via Perth before Dec 06 please get your agent to check up[ that the details are current.