We initially had this same issue described in this post -
www.joomlapolis.com/forum/277-cbsubs-gpl-support/230244-solved-5416-mailer-queues-but-wont-send-mail?limitstart=0#266410
The emails were added to the queue but they would not send, and according to the cron there were no emails to be sent.
As instructed in the above forum post, I installed the latest nightly release for both CB Subs and the Mailer plugin.
After this upgrade, now neither process is working - run mailers, nor process mail queue. No emails are being added to the queue.
I thought perhaps this was because the emails we are expecting to appear in the queue were added to the queue prior to installing the nightly release, so they've been flagged as already processed? I cleared the queue after the installation, so we could then run the mailers and the queue with the latest version.
Could the issue now be that all current emails have been 'flagged' as already queued, and if so, how do we clear the mailer history 'flags'?