I answered my own question. If I had any brains I would eat them.
Please share what you did for other future users who find this thread looking for a solution to the same problem.
I found the same problem, looking for a solution I found un unswer here:
In few words : "It turns out that there is a bug in InDesign that affects the stacking order in interactive PDFs. The stacking order is determined by the order in which the buttons are created. Buttons created first go at the bottom of the stacking order in the PDF. I compare it to a stack of paper: a sheet of paper put down first goes at the bottom of the pile. Then, each subsequent piece is stacked on top of it.
So the moral of the story is that if your stacking order is incorrect in an interactive PDF, remake your buttons, in the order opposite of how they should appear in the final PDF."
Have fun !
P.S. here you have a disscution on that: http://forums.adobe.com/message/5340443#5340443