I am running Exchange 2013 SP1 and just noticed my users are no longer receiving Quota Notification Warnings. I have each database configured to send Quota Notifications "All the Time" since I read that Quota Notification Scheduling was depreciated in Exchange 2013. I found a few articles for Exchange 2010 that stated to add a "CheckWarningQuota" to the registry on the mailbox server, See http://support.microsoft.com/kb/2480474
. However that KB doesn't state that it applies to Exchange 2013.
I have a Mailbox database limits set for the majority of staff, with a couple Custom Mailbox Limits configured.