The plugin is not behaving like the others do in conjunction with: http://wordpress.org/plugins/wp-multi-network/, i.e. in Wordpress MU, with the WP Multi Network plugin. I can manage each plugin separately on each network but not with the New Blog Templates plugin.
Let me give you an example:
I first create a blog template in sophrologues.org and mark it as default, now every new blog I create clones this template.
When I switch to votresophrologue.fr (the other network under the same WP MU installation), I see the template as default but when I create a new blog, it does not clone the template.
I think the issue is coming from the fact that the blog id used when on one network does not exist (or is out of bounds) on the other network.
The solution would be to have New Blog Templates behave like the other plugins, i.e. manage each network separately.
Thanks for your help!