I'm having a similar problem where I want to setup a filter for Plist files in ~/Library/Preferences in /Library/Preferences. I have enabled the system files option in the File Filter input and set my search scope to those two folders, to no avail. I also made sure that there were no exclusions in Spotlight preferences that would break this.
I also tried adding both folders using mdimport like Tyler suggested but this didn't change anything on my side either. One thing to note is that mdfind returns nothing after an mdimport in my case:
mdfind -onlyin ~/Library/Preferences "plist"
Any ideas?
