I've seen quite a few pre-fab boxes that were just poorly done, the silicone was peeling before it was even used. My friend's pre-fabbed box started peeling a few weeks into him buying it.
But, my general beef with pre-fab boxes is that they aren't built to standards. It's just an arbitrary number [for air space] and mass produced... and nearly anything that's mass produced loses quality.
I'd personally rather save money, and "waste" time making a custom box, and know it's done right than buying a pre-fab box that will make my subs sound like Xplodes :|