So I went and renamed my TV show files into the format that I prefer: Series Name 101 - Episode Name.ext
Then in the scraper tool, I changed the File Naming Template and the Title Format (do these always have to be the same format?) to " ^T ^e^S - ^t " and redid all of the scraping for the entire season.
However the result was that only the following episodes scraped properly: 101, 202, 303 etc. The rest remained unchanged.
This is what ended up in the folders for seasons 2 and 4. Note that instead of creating xml files called 201, 202 203 etc, it created files called 102, 202, 302 etc. So the only coincidental cross match in each season was the episode number that matched the series number:
season 2: http://www.freeimagehosting.net/eidkd
season 4: http://www.freeimagehosting.net/kxlyt