[BetterRed]

@Chocky - most everything so far written (in the other thread) indicates something is 'interfering' at the file system level.

Do you use any of the cloud services (e.g. DropBox, iCloud, OneDrive, Google Drive etc etc) for anything else? Or anything like a continuous backup such as FreeFileSynch's RealTimeSync.

By default, calibre on Windows puts the folder that holds its configuration data within the %USERPROFILE%\AppData\Roaming folder. It could be that a parent folder (e.g. AppData) is being synchronised to a cloud service. This might have been done unbeknownst to you by some other software product, some software developers blithely assume that there's is the only software in use.

davidfor's last post in the other thread has some good suggestions, a couple of simple changes you could make to see if they 'stick' are: add a couple of items to the main toolbar and adjust the "Extra spaces to add..." setting in Preferences->Look and Feel

Another thing to try would be to move the configuration data -- e.g. "C:\CalibreData\Configuration" -- and set the CALIBRE_CONFIG_DIRECTORY to refer to that location.

Added : another alternative, assuming you don't convert very large books would be to try calibre portable, its self contained.

BR