In 1988, Purvis et al proposed an interesting hypothesis about silent mutations:Purvis IJ, Bettany AJ, Santiago TC, Coggins JR, Duncan K, Eason R, Brown AJ. The efficiency of folding of some proteins is increased by controlled rates of translation in vivo.

http://www.pandasthumb.org/archives/2007/01/an_evolutionary_1.html

A "silent" polymorphism in the MDR1 gene changes substrate specificity. Kimchi-Sarfaty C (2007) Science.
January 2, 2007