This doesn't sound very likely to me - the only difference between the on-line price and the off-line price for me in the past has been the off-line booking fee, which is a fixed amount.

I guess that the fare bucket you were looking at on-line suddenly filled up before you rang, but if I were you I'd look on-line, get the fare for the exact flights you want, and then phone up straight away. If you get another agent who says what the first one said I'd suggest calling again!