If it is detecting misfires, you still have to fix whatever is causing it even if you can't feel anything. If you want someone to look to see if something got copied over that shouldn't have been you need to post both your before and your after files. Seeing only where it is now isn't much help.
A logfile will also have DTC data in it, under the Details tab (bottom of the channels list).
I don't see how it would be possible to do any of the things you're doing without lots and lots of logging, much less 'oh I'll log it eventually if I find time.'
Took it out to do some logging, drove a mile and realized that it wasn't logging anything. Found out the obd port fuse was blown. Changed the fuse, now the check engine light is off, TCC and everything seems to be working/running perfectly.
Not sure why that fuse would cause problems, I couldn't find any option to log misfires though. Only option under spark was advance?
It seems that the missfire is gone for now, time will tell if that's permanent.