Like Pv says, it sounds like you are running Vista. From the JSGME readme:
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MICROSOFT VISTA USERS: If you are running the Generic Mod Enabler on Vista and are having problems with mods "taking" (the usual symptom is that the MODS folder itself is not created when the Generic Mod Enabler is first run), then simply right-click JSGME.exe in Windows Explorer and select "Run as Administrator". Alternatively, right-click JSGME.exe and select "Properties". In the properties window select the "Compatibility" tab and check "Run this program in compatibility mode" and in the box below select "Windows XP (Service Pack 2)". In some instances you may need to apply both solutions.
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