In a Microsoft Exchange Server 2007 or Exchange Server 2010 environment, the MSExchangeIS Mailbox Messages Queued for Submission performance counter keeps increasing.
When the MailSubmission service submits a message for delivery multiple times, the counter is incremented two times but decremented only one time. This situation can leave the counter with a positive value even though there is no message in the queue. When you restart the Microsoft Exchange Information Store service, the counter is reset.
This is a known issue with Exchange Server 2007 and Exchange Server 2010. We do not recommend that you use this counter for health alerts.