All the web roots are under web, and within those will be several config files at different levels. I am seeing some inconsistent behavior in the indexing. Some web.config files are indexed others are not. In the cases where the file is NOT indexed, other config files ARE indexed from the same dir at the same level.
Splunk UF is running as localsystem on Server 2008
All files have the same permissions and update times. They are part of a CI cycle, so are constantly updated throughout the day.
Is it possible that ones that aren't getting indexed are identical to ones in other directories that are getting indexed? Splunk could see it as a duplicate file and skip indexing. Out of the box, Splunk isn't great at handling this sort of work.
You could try looking into adding crcSalt = <SOURCE> to your stanza, but it depends on your use cases.