I double checked and there is nothing in those folders. Only thing in those folders are my other scripts for DBOX (a plugin for X3 Terran Conflict).Stu, I had two of them show up when I mistakenly copied the scripts into Max 2011's scripts folder. Now I've only got one. Perhaps you have copies of those scripts in folders that Max references on startup?
In my Plugin.UserSettings.ini is this:
[Directories] Additional MAX plug-ins=E:\Program Files\Autodesk\3ds Max 2011\PlugIns\ New Entry=C:\Program Files\Lockheed Martin\Prepar3D SDK 1.1.2771.0\Environment Kit\Modeling SDK\3DSM2011\Plugins\