my best guess would be, long before, at the age of the first hokage, the kyuubi was indeed a freak of nature and that madara, luckily, had the first glimpse of the kyuubi. he tricked the kyuubi with genjutsu (reason why when the fox saw sasuke's sharingan the fox said eyes more sinister than mine) into fighting hashirama but since hashirama had the upper hand, he pawned the kyuubi and took the kyubi as his own in the process...

he then distributed the other bijuus but made sure that the kyubii was within the village's reach... then they found kushina or whatever...
with madara and kushina thinggy, my only explanation is genjutsu...

i dont think madara has the ability to extract the kyuubi in its original form, i do believe that kushina lost control and got transformed into the kyuubi and that when minato sealed the kyuubi, kushina went along coz she was the transformed kyuubi...