When I went into the Ancient Ruins (Tradewinds Skyway between the Dark Jungle and the Gold Monkey) I made sure to go by the life fountain there. When I fled a fight in the ancient ruins, so as to catch up with my team by Hopper, it put me on the Gold Mine docks fountain, not the Ancient Ruins one. After I leveled, up, I used the shortcut to Skull Is. and the life fountain was correctly reset to Avery's Court. After I returned to a friend in the ruins, I revisited to life fountain there. It does not work. My life fountain button still says Avery's court. I'm standing right next to the Ancient Ruins fountain and it is not resetting the button.
I have had this problem too and I am beginning to think it is by design. I am guessing that too many people have used the Life Fountain Goto button to bypass exiting the pyramid and any fights they might get in (although it is easy to do staying at the edge of the walkway to bypass any fighting). There are a few other Life Fountains like this. The one in Monquista City - Monquista comes to mind. Always check your Life Fountain button before pressing it (or you might end up somewhere you didn't expect) by hovering the arrow over the Life Fountain button.