All I can say is think of it... Adrenaline has to calm down sometime, because if it doesn't, mental illness as well as worse physical illnesses can result. I think Yuffie was just at that breaking point, but didn't cross it. A guess, but I think a very valid one. Traversing the entire world more than once over, experiencing the death of a friend, fighting monsters released to protect the planet, fighting everyday mutant creatures due to sick scientific experimentation, doing all that could be done to save the people who would budge in Midgar... Yeah, I think it was everything just caught up to her. Still a guess, though.
EDIT:
I read up the new posts since my last.
Well, the only other thing I could think of is that when her father locked her in a room, she just mentally collapsed - again everything caught up to her. As much as she disrespected her father during the game, she holds Wutai in such high regards. She would never do anything purposely to hurt her beloved land and people.