Mails only sent at cron run

my cron runs every 15 mins but even if I set user notification frequency as 1 hour, the subscription notifications are still sent every 15 minutes.

Are you sure about this? The way it's supposed to work is that the first batch of notifications will be sent at the very next cron run, but the same user should not receive another batch within the same 60 minutes from when the last batch was sent. Other users may run on different quarters, of course.

Testing this requires a bit of careful planning...

Is there a way I can check manually in the database where the send frequencies are stored and make sure they are OK?

Yes, I'd be very interested to get that information. Unfortunately, timestamps are just large numbers in the database (seconds since an arbitrary point in time in the last century), so they're a bit difficult to decypher, but here's what should be happening:

Whenever a notification is sent to a user, this is executed:

    db_query("UPDATE {subscriptions_user} SET last_sent = %d WHERE uid = %d", time(), $uid);

It sets last_sent for that user to the current time in the {subscriptions_user} table.

When notifications are queued, this query

        $sql = "
          INSERT INTO {subscriptions_queue} (uid, name, mail, language, module, field, value, author_uid, send_interval, digest, last_sent, load_function, load_args, is_new)
          SELECT u.uid, u.name, u.mail, u.language, s.module, s.field, s.value, s.author_uid, s.send_interval, su.digest, su.last_sent, '%s', '%s', '%d'
          FROM {subscriptions} s
          INNER JOIN {subscriptions_user} su ON s.recipient_uid = su.uid
          INNER JOIN {users} u USING(uid) $join
          WHERE
            s.module = '%s' AND
            s.field = '%s' AND
            s.author_uid IN (%d, -1) AND $conditions";

takes the user's last_sent and puts it (along with the send_interval of that subscription item) into the record of the pending notification in {subscriptions_queue}.

Finally, those records are retrieved with

    $result = db_query_range('SELECT * FROM {subscriptions_queue} WHERE last_sent + send_interval < %d ORDER BY sqid', time(), 0, 1);

Here, last_sent+send_interval is the earliest time at which that user would want to receive another notification from that subscription item (the send_interval can be different for every subscription item), and the pending notification record is only retrieved (and subsequently processed and deleted), when the current time is past last_sent+send_interval.

This should work, and I'd like to know why you get the impression that it doesn't.

Subscriptions doesn't use job_queue at all. What gave you that idea?

Thanks for wrapping up.

You mean subscriptions_og isn't using the send_interval defaults that you set in subscriptions?

Please report that as a bug in the subscriptions_og issue queue.