I am about to bite the bullet and get a 2006 Rubicon. I have been watching these forums for some time, and it appears that the most prevalant problem with the Rubicon is the tendancy for the display to show error codes and require a re-set. Is this a serious problem? Any other problems to watch for?

 

I havent seen many of them. The old posts you saw, must be reallty old. Are you sure youre not thinking about the ES models (rancher, foreman and recon)? The rubi is pretty bulletproof, and what the button shifts is totally diferent than on the ES.
If youre concerned about the reliability, Ride it alot when you first get it, because the warrentee clock is ticking...you only get 6 months, and you want to make sure you get enough miles on it, to have found if theres an issue, and have it fixed.
I would bet that 95% of all the honda quads, never come in for warrentee work.
If the tranny had issues, honda would have it figured out by a 2006 model, and either fixed it or disconntinued it.
I say go for it