There's a confusing UI here that could be part of the problem, but I'm trying to remember where it crops up (haven't gotten it to occur yet in poking around on a few sample bookings). Essentially, the site shows what looks like a seat map, but it's a generic image, not representative of the actual seats on the flight.

But it sounds like you're doing a search, then clicking the "Seats v" link next to the flight in the search results, and the seats shown there are different than the ones when you select the flight, click a couple more screens, and get to the seat selection page, right? The only times I've had issues there, I've logged out and then back in, and the discrepancies went away.

ETA: I found the glitch I was looking for; if you pull up an itinerary after booking, there's an image of the plane apparently showing available seats off to the lower right of the screen, with a big "View Seat Map" button. The image has nothing to do with the actual seat layout or available seats on the flights in question. I think I've seen the same image show up during booking, but haven't been able to replicate that behavior yet.