Which version of DiRT are you attempting to run? The only time it _should_ run SARA.EXE (the app that checks if the mailstore rights for using ExMerge are there for the currently logged in account) is if the checkbox for backing up messages is enabled. It sounds like either that got checked or there some sort of logic issue there - it should not matter at all that you ran it via TS, that has no bearing on those settings at all, they're just flags in the registry.
Are you running it directly out of the directory it's installed in or via Tools Depot? There was a reported problem where the directory wasn't changing properly when launched from TD - should be fixed but it's worth ruling out anyway.
That particular issue was fixed a few months ago - if you haven't already be sure to download the latest version off www.CiscoUnityTools.com. If you're still having a problem with that version come back with some more details on exactly what you're doing and what you're seeing.
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