New Blog Templates - Breaks Main Site's Template

I have a multisite with 19 templates (1 main site, 5 free site, and 13 premium). This multisite uses Pro Sites and New Blog Templates, among many other plugins. Users do not have access to the main site's template.

Problem: Every so often, a new user creates a blog and the main site adopt the new blog's template (a free template) for a minute or two. It seems like a problem with caching.

Any ideas what's going on here?
Have you seen this before?
Any ideas where to start looking, or how to solve it?