I think I might be experiencing this as well.
When I activate the plugin and go to convoke.info/stuff I get the godaddy 404 error page.
With the plugin disabled, convoke.info/category/stuff works fine.
The reason I’m chiming in on this thread is because convoke.info USED to be multisite/network. When I was developing this new theme (and testing out the no category base plugin) on a DIFFERENT test site (NOT network/mutlisite/mu) it was working fine.
Hopefully I’m being clear.