Nice call! Found out what was causing the problem by your advice: A program called Linux File System for Windows (by Paragon Software). Used it to transfer files to/from Linux USB drives. Don't use it anymore but it was running in the background. Removing it seems to have totally eliminated the issue. So, the issue WAS with syncing software.
Thanks for your help, really appreciate it!
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shadowblind's post in Launchbox Folder constantly returning to 'Read-Only' was marked as the answer