I'm attempting to make changes to my Search Paths but the settings do not save.  I'm having the same problem when attempting to change the path for the Hole Wizard and Toolbox folder path.

System Options > File Locations > Seach Paths

System Options > Hole Wizard/Toolbox

System Info

Win7 x64

SW 2012 x64 SP3

Logged in as an Admin, attempted "Run As Administrator" command when opening SW.