Ok so I could get autocron to work but not cron.
After hours and hours of debugging I figured out the imap calls weren't working. Turns out on Ubuntu (I am guessing other places as well), there is a php.ini for apache and one for command line. The apache one had the correct extensions line but the command line one didn't.
The line is
extension=imap.so
hope this will help someone not waste as much time as I have.
