Alex Boone, who made a nearly seamless transition from tackle to guard two years ago, is unhappy with his contract and may not be part of the 49ers' Organized Team Activities that began today, sources said. Boone went undrafted in 2009. He signed a four-year extension in 2011, and he has two more years on the deal. The 49ers have an unusual situation on the offensive line in that their top player there, left tackle Joe Staley, signed a long extension early in his career and is making only a modest salary – $2.7 million in base pay – this season. Therefore it's difficult to pay other worthy linemen like Boone and fellow starting guard Mike Iupati, more than the left tackle. (The team already hiked up right tackle Anthony Davis' salary in the offseason).