Notifications not being sent out via cron

I've just found this bug too. Behaviour is exactly as you describe - manually processing the queue with "Run process" works, waiting for cron to do it does not.

Turning "Immediate sending" on in the "General settings" (admin/messaging/notifications/settings) also fixes the problem, but is not desirable for a number of reasons.

I had something similar happening...
I failed to notice that there were 2 areas for setting permissions in admin/user/permissions

Permissions: notifications module
(had to have authenticated users 'maintain' and 'manage' own subscriptions)
and
Permissions: notifications_content module
(had to have authenticated users 'subscribe to content' and 'subscribe to content type'

ALSO

had to go to
admin/messaging/notifications/ui
and select 'Visible subscription types: Content Type'

ADDITIONALLY

had to go to
admin/messaging/notifications/content
Enabled 'Set up for each content type on Administer Content Types.'
Global thread option = Content type. Subscribe to all content of a given type.

FINALLY
had to enable notification subscriptions for certain content types.
I wanted to send email updates for events, so had to go to admin/content/node-type/event
Allowed subscription types: = Content type. Subscribe to all content of a given type.

All that said...
If you go to my account -> user/1/notifications/nodetype (or user/whatever#/notifications/nodetype)
You should be able to select check boxes for the content types you would like to subscribe to, as well as the interval of email updates (hourly, daily, etc.).
I had a few hundred users on my site, and just updated everyone's account by hand... but you might be able to use Rules or some other method to change old users... still not sure if new users will automatically receive updates even though admin/messaging/notifications/content -> Set all users to "autosubscribe" by default is selected.

Hope this helps...

Messaging 6.x-2.2
Notifications 6.x-2.2
Organic Groups Notifications 6.x-2.1
drupal 6.16

No notifications are being sent out, I'm manually running cron, and under 'Recent log entries' there are entries that show all the notification messages but they are not actually sent. I've checked by junk mail and nothing there either.

I've followed the settup in #3 and still no luck.

UPDATE:
My bad – I had 'debug' mode on which blocks notifications

Where is the debug setting???

yourdomain.com/admin/messaging/settings

Sory, but I can't see any debug option :(

Debug is shown only if the Messaging Debug module is active.

closing