Did you publish a new package after checking the boxes for the other channel stores? Any time you make updates to a channel, even if it's just channel store properties, you need to submit/publish a new package. If there weren't any changes to the channel, you can just re-publish the same package as last time.
My Channels: http://roku.permanence.com - Twitter: @TheEndlessDev
Instant Watch Browser (NetflixIWB), Aquarium Screensaver (AQUARIUM), Clever Clocks Screensaver (CLEVERCLOCKS), iTunes Podcasts (ITPC), My Channels (MYCHANNELS)