Came in this morning, and the indexer is working as it should.
I think it was just a large file and I wasn't giving it time. I didn't think the indexer was under a heavy load at the time, but the clue was the WARN message:
"10-06-2015 15:24:37.496 -0500 WARN TailReader - Enqueing a very large file=/var/log/squid/access.log in the batch reader, with bytes_to_read=878207660, reading of other large files could be delayed"
Thanks Anekkanti, lesson here, RTFEL (read the fine error logs) for clues.
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