I feel you. I had an identical experience last year around this time. Wasn't a startup situation, just a very small shop run by a hot ninja who was trying to palm off a quarter of a million lines of undocumented byzantine code without bothering to mentor or even explain the business processes this thing was designed to satisfy. Bleh.

I was able to land a gig with a small shop doing work for some incredible clients filled with brilliant people that know their product back-to-front and management that polls the developers for input throughout the project life cycle. Needless to say I've never been happier.