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jamesgl - I sent you an email
AutoRuns
If you're minded email me the ARN
Drop Text File into a Book (Details)
This is OK on 32bit and not OK in 64bit - that's what I expected
Total Commander
Red Herring - shouldn't cause problems, besides same behaviour if file is drag 'n' dropped from Windows Explorer - works in 32bit but not in 64bit
Temporary Directory
Same behaviour 32bit OK, 64 bit crash - so its not a Temp permission error masquerading as something else
Manually Create Folders
Pseudo author and book folders and files can be created - eliminates the possibility of a corrupt MFT, which was a highly unlikely cause - NTFS is NTFS, is NTFS no matter what the bittedness of an application
System Restore
To repeat : replacing windows inline or in its entirety are last resort options. You have a working solution with the 32 bit version, and if push comes to shove there's the calibre portable option.
Configuration Data
This had already been eliminated - also I can't recall seeing an instance of 64bit
crashing that was fixed by resetting the config data back to defaults. Occasionally there are glitches that can be fixed by editing or deleting a JSON file, but I can't recall a freeze/wedge situation - but even my memory sometimes gets parity errors

Close all other programs
60 processes is about right for the 'minimal set' if you include the Windows processes
There's a check box at the bottom left of Task Manager Show processes for all users. if you turn that off then after Exiting all programs there shouldn't be much, some applications have 'background' processes, eg Evernote Clipper, after terminating them I have 15 processes (bluetooth, video adapter, explorer, disk health monitor, AV etc).
Your tests to date, and the fact the 64bit fails in Safe Mode makes me doubt it is a 3rd party program
Ignore Plugins
Well it looks like its not a plugin.
** Replacing Windows Explorer
This is a non-issue with Total Commander - its probably a non-issue with X2 and Dopus.
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james - can you confirm that conversions are OK with 64bit ?
There's one other thing you might like to try. There's an Environment Variable, CALIBRE_NO_NATIVE_FILEDIALOGS, that if set to 1 will cause calibre NOT to use the native (Windows) file open/save dialogues (it will use some built in dialogues). See
Customizing calibre — Environment Variables
Happy New Year - BR