Two thoughts come to mind, if in the system notes the type for the first field change is Set and the second one is Change, you can add that in the criteria of your search, for instance, in your criteria, you can have

System Notes : Field is yourCustomField

on one line and the second line have

System Notes : Type is Change

and that should only bring back results of that field if it has changed. My second thought is pretty similar, but instead of including type, just have

System Notes : Field is yourCustomField

then on the criteria page, under Summary, choose Summary Type Count, Field is `System Notes : Field and Description

is greater than 1

.