Yeah, thats weird cos my project are saved in the My Documents folder and all shelves and MELs and in the [what you called] the 'defult maya folder'.

I just re-installed maya to see what happened and it's still the same. I guess it dosen't matter that much, it's dosent really harm maya i think. The reason why i asked was because i was wondering if that has anything to do with why i can load the GI_Joe MEL

Thanks for your help