You might be running into married segments (there are seats open from A-B and B-C, but when sold as "A-C", the seats disappear). They do this as part of revenue management, hoping to squeeze more $ out of folks like you. Don't worry, all the airlines do this, though.

If you play around with your timings a little bit, I could find some trips in true economy (V/M class or something) for about $650. Not a huge savings, but it might be worth it on your expense report. You can do even cheaper by flying the DL-codeshares, but alas no upgrades. Good luck.