I suspect in your case it may be another add-on by some author/vendor that is causing this problem. You had asked about Freeflow - do you have that installed? One quick way to isolate your problem is to disable all third party scenery enhancements so that you only are running the default scenery to see if the problem goes away. Then add in FSG mesh next, and finally UTX.
Hopefully you do not have a third party add-on installed into one of the default FS scenery directories or there won't be any way to prevent it from being pulled into the scenery indexing other that to find the files and move them out of the directory.
(oh, and it is Scott Gridley who is the Freeflow author. I have been watching too many Vacation movies recalling a name like Griswald)