I'm using SCOM 2012 R2 and have configured an alert generating rule to create alerts when specific events occur in a windows event log.

The rule works fine, alerts are generated as expected.

I have also configured subscriptions/subscribers/channels to send notifications via email and SMS (via script in command channel) however even with the criteria set to send on all alerts, I only receive notifications for alerts generated by monitors (so I know the subs and channels do function)

It seems like some sort of workflow issue where alerts generated by a rule fail to create a notification.

Is there any logging I can enable to see what's happening here? 

Any other ideas?

In System Center 2012 Operations Manager, the alert notification will be sent when the alert first meets all criteria, regardless of resolution state, unless resolution state itself is a criterion. If alert suppression is enabled for the rule or monitor that raises an alert, only one notification will be sent when the subscription criteria are first met. No additional notifications will be sent until the alert is closed and a new alert is raised that meets all subscription criteria.  PLease check
1) whether your rule has trun on alert supression
2) Close the alert, craised by rule,  and do it again

Roger