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I've created a windows service which silently mounts truecrypt volumes via command line. A couple issues have arose however; although the volume mounts correctly it won't show up in windows explorer unless I open truecrypt and manually click "refresh drive letters". Second, I keep randomly getting messages saying that Windows intereactive services has detected a dialog, and if I accept it will show truecrypt in some alternate desktop. What should I do to fix these issues?

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You are running into Session 0 Isolation, where all UI elements from a Windows Service are shown on the "alternate desktop" you came across. The Interactive Services dialog can be disabled, but think it through before doing so.

Are you running your service in a regular user account? And is it the main TrueCrypt window that is coming up?

CoreTech
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