Pronterface runs slic3r from it's own directory as default, this will most likely be something like C:\Program Files\Pronterface\Slic3r
Just rename this to something like Slic3r_old, and copy the new version of Slic3r to the Pronterface directory.
But after Slic3r started having selectable presets for slicing settings, I found that it is better to just start Slic3r, slice , export, and then just load the gcode in Pronterface, as the presets isn't supported in Pronterface, at least not in the version I'm using.