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kjdavies - those temporary files should have been deleted as it counted each book.
By default calibre uses the default location for temporary files (e.g. on it's Windows C:\Users\<users>\AppData\Local\Temp), and it uses it extensively, e.g. when adding and converting books. It's pretty good at cleaning up, but remnants can get left behind that normal 'system cleanup' processes take of.
You can give calibre a dedicated folder for its temporaries on another drive via the CALIBRE_TEMP_DIR environment variable, see
User Manual: Environment variables
If you give calibre a dedicated location for its temporaries you'll have to make provision for any additional cleanup.
Curious - what format are the comics? I only count words and I never run Count Pages against CBZ or CBR (or audio/video formats etc). Maybe the plugin needs an Exclude Formats setting.
BR