New Blog Templates loses settings

Every now and then, the New Blog Templates plugin loses its settings. I'm not sure why it does, I only tend to notice it when a new site is created on the network and discover that my cleverly planned template was not applied.

Does it retain its settings through a deactivation/reactivation sequence? (aka plugin troubleshooting dance) I also recently updated it for the latest WP, would it lose its settings through an upgrade?

It's happened before too, but I never paid much attention to it, thinking it was something I did, but this is now the third or fourth time and I've had to reconfigure the settings and assign default templates. Has anyone else experienced this?