MS Exchange chains the execution of the enabled Transport Rules in priority order. The placement of the Analytics Support Exchange Transport Rule relative to the other Transport Rules is significant. Depending on how they are defined, Transport Rules that are executed before the Analytics Exchange Support Transport Rule might affect the emails made available to the Analytics Exchange Support Transport Rule by Exchange.
How Rules are Ordered
The rule with a priority of 0 is processed first, followed by the rule with a priority of 1, and so on. You can change the rule priority by adjusting the order of rules in the EAC or changing the priority of individual rules. For example, if you have one rule to reject messages that include a credit card number, and another one requiring approval, give the reject rule a priority that causes it to happen first, and stop applying other rules.
All messages in your organization are evaluated against the enabled mail flow rules for your organization. Rules are processed in the order listed on the Rules page in EAC, or based on the value of the Priority parameter in the Shell. Each rule includes an option for stopping the processing of more rules when the rule is matched.
Reference: Microsoft TechNet