During the endgame after Ultimecia, we see Squall trying to get back to his own time from the time compressed world. He tries to focus on his memories of Rinoa, but they appear fuzzy and unfocused, and whole sections of them black out. Is it possible that the corruption of these memories is the memory-blocking effect of the GFs reasserting itself? He can't focus on the memories because the GFs are blocking them out of his mind. Instead, he winds up further back, to a memory that had been lost to them once, but then rescued when he was reminded of it. Perhaps the memories of the orphanage, having faded once, were protected from fading again, or just hadn't faded yet.
I'm sorry if this is an old idea to some of the posters here, but I hadn't thought of it before because the memory-wiping effect of the GF is mentioned so little in the game. But it seems to me that it would fit fairly nicely with what happens.