Hello,
I've proposed two feature requests which should help with message indexing:
http://portal.smartertools.com/community/a86318/feature-request-adaptive-indexing-based-on-cpu-and-maybe-disk-queue-length.aspx
and
http://portal.smartertools.com/community/a86319/feature-request-indexing-based-on-webmail-usage-perform-first-indexing-when-user.aspx
Can SmarterTools dev take them under consideration? IMHO Indexing service should be working better (I have also some customers complaining about search results not returning all messages which should be returned).