Oh! You're right. The "Flag: Unknown" is set by defeating Edge's parents, since Rubicante appears after that I must have confused the two.
Ah, new version? I'll check that out first...
Hmm, looks like there is still the "one off" error, presumably caused by the "Opening the Sealed Cave??", things appear to be thrown out of order when you reach the Feymarch Entrance Event, the flag there reads "Obtaining the Dark Crystal", when it should read "Feymarch Entrance" I'd imagine, meaning that the proper flag that activates when Rydia rejoins should be "unknown" and "Rydia Rejoins". To note though, the "Opening the Sealed Cave??" is used in the actual "Kain Stealing the Dark Crystal" event, which is also one off, I imagine then that one of the "Sealed Cave" flag copies is causing this error.
Now as for your fix...
It works perfectly! I am curious to know how you fixed it! That is quite an impressive work, may I add to have it read each instance of a "loaded map" for the proper message and NPC layouts!