Feature not activating programmatically, only when clicked

I downloaded the Feature Manager http://spfeaturemanager.codeplex.com/

My question isn't about the feature manager specifically..I have a feature I wrote which deploys and swaps a master page in a site collection. When I use the feature manager to turn the feature on or off, it does change the status in the Site Collection Features list but it doesnt actually do anything. If I click in the Site Collection Features on/off it works fi开发者_StackOverflowne. Any thoughts about what the issue could be. Obviously if its an issue with the feature manager I wouldn't expect an answer here, its just weird that in sharepoint the feature says its activated/deactivated but it isn't actually.

I would suggest use stsadm commands to activate feature and check if it works

stsadm -o activatefeature -name <> -url "http:\localhost"

and if it succeeds please post a bug on http://spfeaturemanager.codeplex.com/