The pre-set auto-org function is great if you have a fairly simple structure and you make "certain" it's set correctly.
However, if it is complex and/or dynamic, it may not be such a good idea.

Thanks all. It was moving the files via Auto-Organize to a very similarly named folder on my system. I guess I'll have to figure out if I want MM to control about 50k song files and trust that the file names are formatted like it wants. O r I can keep that feature off and control it myself....

I don't have this situation.Maybe It's just for few people.

Check Tools --> Options --> Library >Auto-Organize to see if it's enabled and where it's sending the files.

Also, experiment by finding a file within MM then using Add/Rescan on its directory. The file should still be displayed in MM so you can then right click on it and choose Find More from Same --> Folder (Explorer). That will show you were the file is moved to.

I'll give that a try tonight and see if it does the trick. Can't remember but I probably have been "cheating" my way around it since the re-build and possible re-shuffle since then.
Thanks

[quote="pedro67g"]...and my old library location isn't even valid with the new set-up. I'm not sure how to edit where MM should be scanning[/quote]

Ok, so you are moving stuff outside of MM? ...of which it is recommended to use Folder Monitoring.
However, since you rebuilt your system and recently started using MM again(?), the recommendation for that is to first follow: [url=http://www.mediamonkey.com/wiki/index.php/Moving_MM_to_a_new_computer]Moving_MM_to_a_new_computer[/url]. Notably, the last section.

[quote="MMFrLife"]It's happened to you in several recent versions?[/quote]

"Recent versions" meaning I always update when new versions are available and it has been happening for a while.

[quote="MMFrLife"]What evidence do you have of that?[/quote]

Evidence is that I have an explorer window open when I add/rescan from that folder I see the song files disappear. I am assuming they are deleted but could be wrong.

[quote="rivorson"]Do you have Auto-Organize enabled? It's most likely that the files are just being moved.[/quote]

Good point. My system crashed about a year ago and I rebuilt everything (from power supply, motherboard, processor, drives, etc.) so the system is reconfigured and my old library location isn't even valid with the new set-up. I'm not sure how to edit where MM should be scanning as I thought it was a meta program that watches over the whole system. My normal method is using the file tree to navigate to my new library location and choose music from there. Any advice would be appreciated. Thanks.

Do you have Auto-Organize enabled? It's most likely that the files are just being moved.

That's odd. I've never had that happen.

What evidence do you have of that?
In the title of your post, you say Hard Drive, but in the post you say from the Library. Can you elaborate?
[quote="pedro67g"]but in the recent versions[/quote]
It's happened to you in [i]several[/i] recent versions?

If files disappeared, did you try to search them with windows search or even MM search?
Did you check MM's Entire Library (tree) > Location > Folder(s) with media files?

Luckily I back up everything, but in the recent versions when I add/rescan MM actually deletes the file from my library. Does this happen to anyone else?