FWIW, I've used vacations to go for booking all my cruises so far. I use a specific agent there (that my parents actually recommended, she's the one they've been using for theirs). I can't complain about the service that I've gotten from her. (Heck, she was even in her office the Monday after a hurricane went through Houston which is where they're based).
Now, that said, I don't know that I'm saving much if anything over what I could find myself, but I'm also not paying more than I could really find myself. She's also helped out in a couple of trickier bookings (including one that probably netted her no commision at all), so I feel a little loyalty to her as a result. But I'm probably one of her easiest clients to deal with because I generally know exactly what I want, down to cabin number, before I call her.
As for the OP's situation, I don't know that the prices they list on their site are updated as you look at them, so it's entirely possible the prices change, cruise lines certainly do that. And I've certainly seen some crazy pricing at times (my upcoming alaska cruise, when I booked it, BD balconies were running double what a BC balcony was running, even though theoretically BC is the better class).
(Oh, and cruiselines can do some really funny things for people that aren't in the US too. Prices you see on a US website might not be allowed to be booked by someone not in the US. Specifically, the vacations to go website says "Costa, Holland America, Oceania, Norwegian, Princess, Royal Caribbean and Star Clippers no prohibit US travel agencies, including Vacations To Go, from selling cruises to customers who do not have a residence in the US or Canada).