OK, so the first questions is: did you ever create folder sets, i.e. define one more password for Espionage, if you did, it might be that there is a folder set to auto unlock in that other folder set, could this be possible?
The other thing would be, to simply set the value to 0, and it will not ask for password any more, till you again set one folder to auto unlock. It might indeed be that in some combination of events the preferences were not updated correctly and the value remained on 1 for no good reason.
To set the value to 0 use
defaults write com.taoeffect.Espionage3 TENeedsAutounlock 0
Then try to launch Espionage for few times, see if it stays OK, then again try to set, unset some folders and see if it behaves (if you wish to play with this further).
Thanks for your feedback and time for testing.
Rgds
Zsolt