In splunkd.log I see a few lines like:
BatchReader - Removed from queue file=...
It's not a warning or an error, but is it saying that some events aren't indexing?
Try adding crcSalt= in inputs.conf
I think that means the file parser reached the EOF and doesn't have any more work to do for now. If the file has log data appended to it later the parser should notice that and re-add the file to the queue.