Thanks to both posters for their quick response.
I've checked my stats on Geocaching.com again today - still 4 over. I even tried deleting the original log but it only took one off so I've re-logged. Looks like there's no solution.
Interested to hear you both feel it's OK to log a trackable twice if you find it in a different location. I'd always assumed it would be wrong, like trying to log a cache twice, but I understand where you're coming from.
It would be nice if I could have kept the numbers on Geocaching.com and GSAK the same for when I use BadgeGen to produce stats for my profile page but I'll just have to keep a record of the "extras" when updating.