Large proteins which cannot enter these pores pass around the outside of the beads. Smaller proteins which can enter the pores of the beads have a longer, tortuous path before they exit the bead. There are two extremes in the separation profile of a gel filtration column. See the following fig. The spread also somewhat depends on the elution position.
Larger proteins elute fasters, thus have less time to spread due to diffusion.
More over, smaller samples have higher diffusion coefficients, thus they spread even more. See the following figure. The choice of type of beads. Unfortunately, smaller beads require higher pressure to force the liquid down the column. Recently developed Supurdex in Pharmacia is good for this purpose.