One of the many issues the NFL and NFLPA dealt with in their 2011 collective bargaining was draft picks holding out early in their contracts. The new CBA set it up so that picks could not re-negotiate their contracts until after the third year, and UDFAs can re-negotiate after their second year.
The 49ers are in no rush to hand out contract extensions for their 2014 class, which makes sense given the new coaching staff and front office taking over. We might see some deals before the end of this season, but I doubt we see anything of note between now and training camp.