I HATED that!!! I swear, I wrote down the GFs I had equipped to each character, then when it comes time to switch with Laguna & Co. I lose the paper and have to write it down again for next time I go through the game! I can never get the junctions just like I had them before :kaocry2:

They go away when you go from Squall to Laguna but when you go back to Squall they stay how you junctioned them during the dream sequence.