I have to "include non-indexed files" after every update...

Every time a new version or update of Bridge, I have to run a search and include "Non-indexed" folders. 
This is pretty inconvenient as I am dealing with dozens of folders and thousands of files. 
Once I do the very long search, any future searches go pretty swiftly, but then there is another update and its back to square one.

Am I the only one or am I doing something wrong?