@AlexG Hey! Sorry, I missed your issue. I'm no longer actively maintaining any of my plugins, but feel free to poke me on GitHub any time.
As far as re-indexing, it does this exactly once. When the plugin is installed. Normally, there should not be a need to do it more than once, but if there was any error during re-indexing, or if a very early version was used, it could be required.
If new topics are now correctly sorted, then everything should be working fine. Otherwise, poke me again on github and I'll take a peek.