Deactivating plugins network-wide not working

Hello all,

Just upgraded my WPMU to WP 3.0 and I’m noticing a lots of errors in my logs files with “headers already sent…” all related to some plugins. I’ve tried to do a “network deactivate”, but on any sites where I manually activated the plugins, the network deactivate is not working. I’ve also tried to use the “Proper Network Activation” plugin, but still no luck.

I’m specifically trying to get rid of Brian’s Threaded Comments, as it’s no longer needed, and wp-grins which is just not working with the new version of WP.

So is there a preferred method for removing plugins in this new version? I really don’t want to have to touch each blog as I’m not sure which ones have which plugins activated, and trying to delete/deactivate the plugins and then do the “network update”, which I figured would touch each blog, see the plugin was deleted and disable it automatically, also did not work.

Thanks for any help.