I ran into this problem when booking my trip this year. Pop showed availability online but none was to be had on the phone. Hung up, and then booked it online. Called back, got another CM, and he explained that the website (when working...) shows any cancellations or openings sometimes a day before it shows up for them, the phone folks. True or not, I don't know, but it sounds plausible. When trying to move to CBR, the same thing happened. A water view room that hadn't been available before showed up online on a Monday, nothing available according to the CMs on the phone. Tuesday it was still online and also on the phone.
If you see something you like online and it's not on the phone, I would wait to book it over the phone, either way. Better safe than sorry.