All i know that is when editing Moi.ini in Notepad++ instead of giving it a shortcut to the exe it started working again.
The newest files started to pop up accordingly and in order again when layed in Moi3D folder.

Ill guess the permission-part is a big part of the problem. I was unsucessful to give Moi.ini all authority status.
So i gave up the search for an all permit (Admin-rights to moi.ini).
It ended with giving Notepad++ all the admin-rights to the moi.ini instead.

It worked for me, although this is the first example not sucessful with giving permits and admin-rights to
individual folders or files.