You are using calibre portable.
calibre portable sets the configuration directory (which contains, among other things, the plugin) to a portableized directory. But only if you use the main calibre program launcher.
When you run ebook-viewer on its own, it doesn't set the environment variable pointing to the portableized configuration directory
and ebook-viewer doesn't see the plugin in the default,
installed location for the configuration directory.
If you set the CALIBRE_CONFIG_DIRECTORY variable as instructed
HERE, you can duplicate the effects of the calibre-portable.exe launcher, and make the ebook-viewer portable as well.