>Text-based conversations are not in-person conversations!

My guess is Facebook is wants its messaging system to be farther towards in-person conversation on the scale of information-richness.

>"seen" is an impossible flag to get right

I'll agree with you there, but I think most cases would be handled quite well by setting "seen" iff the user interacts with the Facebook window after the message is displayed. This would handle situations where the browser is in focus but the computer is unoccupied, switching users, shutting down, etc.