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What happened?
When upgrading to BlackBerry® Enterprise Server 5.0 SP3, a prompt titled Upgrade Issues may appear that contains wording similar to the following:

The setup application found the BlackBerry MDS Integration Service on the following computers in the BlackBerry Domain:
<ComputerName>

Before you can continue the current upgrade process you must un-install the BlackBerry MDS Integration Service. For more information, see the BlackBerry Enterprise Server Upgrade Guide

Why?
MDS-IS is not supported in BES 5.0.3 any more. If you want to upgrade BES to 5.0.3, then dispose of MDS-IS and its associated MDS-Runtime applications. Stick with BES 5.0.2 with MDS-IS or explore other ways of developing + deploying BlackBerry applications here - BlackBerry - BlackBerry Developer Zone

Source: KB25012-"Upgrade Issues" prompt appears when upgrading to BlackBerry Enterprise Server 5.0 SP3