I wanted to take a video to show this, but I don't know how to take a video and then post it. So instead I'm gonna post Step-by-Step pictures and show exactly what's happening, and point out what's wrong.
Step 1:
Select Location Node Folder containing songs from a single CD, currently in FLAC format. (See below of what's wrong with this picture). Notice these are the "Title" Names that appeared after I ripped these tracks from a CD and before I entered in the proper metadata information.

Step 2:
Select Location Node directly above (Note everything is fine in this view)

Step 3:
Go Back to Previous SI-5006 Node (Take Note that all "Title" Metadata is displaying as expected now)

Step 4:
Use Keyboard Short-cut keys <CNTL> + <A> to select all currently viewed Tracks. (Everything still ok here)

Step 5:
Goto track view area, Right Click and select pop up menu item "AUTO ORGANIZE FILES" (see below for all the things going wrong here)

Step 6: Click "Cancel" in Auto Organize Files pop up window since this is not displaying the expected results

Step 7: Go Back to Step#2, and continue to loop with the same results each time.
So, after experiencing this the 1st time, I closed out MM and restarted, and found the same results.
I then went to FILE>MAINTAIN LIBRARY>OPTIMIZE DATABASE(COMPLETE).
I'm still getting the same problem, even after having MM going through and optimizing the database.
Is there anyway I can get the Metadata to stay???? What the hell is going on here???
* I already went through and checked the file properties and they are NOT set to Read Only.