Does Eclipse under-estimate the game length, or are we playing it incredibly slowly?
I think games companies often estimate the time based on players who know the game. My first few plays of a game will often run long compared to the estimated time on the box, but my tenth, fiftieth or hundredth play will often come in around the box estimate (or less).

Eclipse is a big game with lots of things to take account of (various technologies, balancing your empires, etc.). I'd expect your first five or ten plays to require extra thinking time while you get to grips with it.