Well, here's what I have to say here...
I love plugin commander, very handy and helpful thing. But...
It doesn't work with some plugins as expected
For example, WP e-Commerce (http://www.instinct.co.nz/e-commerce/)
When I activate it via Plugins menu in WPMU - it works just great. When I activate it via plugin commander - it does not create default option in the database and WP e-Commerce doesn't work.
NextGEN gallery (http://alexrabe.boelinger.com/wordpress-plugins/nextgen-gallery/) - plugin commander causes problems in WPMU during signup if NextGEN gallery is set to auto-activation.
Great Real Estate plugin (http://www.rogertheriault.com/agents/plugins/great-real-estate-plugin/) - if activated via plugin commander won't allow to change settings.
So, if you experience troubles with plugins not working - check if they work without plugin commander.
BTW, dropped a message to author of plugin commander. Not sure what he did wrong, but it really messes things up :(