try to put the Ninja_UV.mel not inside the scripts folder. The previous bug was related to other scripts loading and conflicting with Ninja_UV. Try to copy the mel file to a temp folder and source it from there.
If you have the Ninja_Dojo White Belt you can put the mel file inside the Ninja_Dojo folder. it should automatically create a button in the Dojo.

I have the same issue, every time I restart maya. I need to re-source it every time. I've moved it to other locations, outside the maya folder in My Documents.. Using maya 2012 x64 first release on windows 7

when you create a button for it just put the source line in.

source "C:/Mydocuments/Ninja_UV.mel";
Ninja_UV;

use these 2 lines .. just make sure the path correct in the first line