I know that there have been some billing system problems with automatic payment detection. This was a feature we wanted in our systems and this is why we migrated to this new billing system at the beginning of this year.
We've now done some tweaks and are able to fix automatic payment detection for accounts that were transfered to the new billing system back in January 2009.
We still check all payments manually as well; however, it can take some time to complete this process.
If you're having any problems at all please send us an email to [email protected] or open a support ticket.