launchd still thinks it should load InstantScan, even if you've turned it off. Try the following in Terminal to stop launchd from trying to load retroisa now, and turn if off for the future:
sudo launchctl unload /Library/LaunchDaemons/com.retrospect.retroisa.plist
sudo defaults write /Library/LaunchDaemons/com.retrospect.retroisa Disabled -bool true
Then check to see if it's worked:
sudo launchctl list | grep -i retro
...and, with any luck, you'll see just retroclient and updater listed and not retroisa.
How are you choosing those folders -- are they "Favo(u)rites", or are you using rules?