There definitely is still a problem, I just updated the case notes. After re-indexing I get 248 nodes with the word "community" in them, less than 1800 lines of output from the search. However, I created a Compliance policy that checks all the nodes for the word "community" and I get nearly 3000 as expected.
I was also not understanding how search works completely.
The wording on your NCM search page is very misleading… I think it needs to be changed, or better yet, the way your search works needs to be changed. When it says “Search the last downloaded config from each Node only”, what it really means is “Search the last downloaded config for each type of config”.
Ie: If I do a search and there is a “startup config” from 1/1/2014 and 50 more recent “running configs” from dates ranging from 1/2/2014 to 9/5/2014, your search will search the last startup-config from 1/1/2014 and the last running-config from 9/5/2014 and return results from both if it gets a match. In general, I don’t think many network admins would want these results, the “startup-config” is stale, there have been multiple running-configs more recent for that device, it should NOT be included in results based on the wording given below. I only want to see results from the “last downloaded Config for each node” as it states. Now if I want to search the last startup’s, it’s nice having that option too, but not by default when the "Search the last downloaded config from each Node only" is set.