Find Missing Samples even if Hal knows where they are.

It seems every time I load an instrument in the Load/Media bay section or in the browser, HAL needs to “Find missing Samples” even if I just had that instrument loaded a few minutes before. The “Missing Files” path in the top of the “Find Missing Files” window is exactly where the files are.

How do I teach HAL to hang on to previously loaded instrument file paths and or can I teach it to find all of them?

I have trashed my “mediabay3” file in my prefs and re-scanned the disk in HAL with no change.

What am I missing, or which one of these procedures should work?