I was able to recreate the behavior. I created C:\Users\Username\Downloads\test.bat whose contents were:
REM 12345
PAUSE
I then Saved to Disk in a Single Directory and selected the "C:\Users\Username\Downloads\Test" folder.
After the books are saved to disk, I get a Command Window with:
C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Apps - General\calibre 64bit - E-book Management>rem 12345
C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Apps - General\calibre 64bit - E-book Management>PAUSE
Press any key to continue . . .
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