Same thing happened to me
I was traveling with my wife 2 weeks before xmas in 2007. I had booked my flight several months in advance, we were going from LAX to JFK. When I booked my flight I also signed up for their elevate program. A week before we left my wife wanted to print up an itinerary, well thats when she noticed a change. The flight numbers were the same but the flight was pushed from 2100 to 2300, putting us in at 0730. This sucked because we had to be in Connecticut by 0800. I called them up and asked them if it was correct, and when did it happen. I told them that I was never notified, I signed up for their program and they had my phone number, email, and mailing address. They had 4 weeks since the chance to notify me and failed to due so. They created a huge inconvenience for us. They said the would give us a full refund, but at that time after looking at several airlines, it was going to cost to much to change. So we stayed with Virgin, their website said the flight was on time right before we left for the airport, when we got their we found out otherwise. They told me the flight was delayed an hour due to weather, having working in the industry at the time, I knew that was crap, their was no weather in SFO, LAX or JFK, after talking with the supervisor who had checked my luggage, he admitted it was due to crew rest, from the previous days weather.
Their was just a lot of confusion with their IT systems, I see no a lot has changed. I enjoyed the flights, but their ability to deal with the business on the behind the scenes activity needs drastic improvement.