I've used the Chrono Cross roms here on this site extensively- doing a first runthrough.. NOT 'not-saving-Kid'- just, 'getting Glenn'.. and the next, saving Kid/Schala.
Point is, I never had the issue... most likely, man- you gotta reset the game and load it from memory card; it really might just be a bad sequence of events in the coding hierarchy.
OH I KNOW WHAT IT IS! DUDE! You gotta try callin the flute from where the hole is, or something. Or try callin it again from where that beeba with the fruit first appeared! Something like that!
Currently playing:
~~ Pokemon Emerald on VBA ~~ Star Ocean on ZSNES ~~ Tales of Phantasia on ZSNES ~~ Star Ocean: The Second Story on ePSXe ~~ Breath of Fire III on ePSXe