WWWWWOOOOOOO HHHOOOOOOOOOO
I've been intermittently having this problem of double cutting for a looooonnnng time. I'm designing in Illustrator CS5 and "save as" an EPS file. It didn't happen every time but it would drive me NUTS because it would pull up corners on small details and even what I could weed had these little stringy pieces left over. This may not solve your problem but it has finally put an end to a source of misery for me!!!!!
In the stroke panel you can choose to stroke the "center, inside or outside" of the object. If you use any option other than "CENTER" for the stroke you will get a double cut!
So Simple. Thats why I was only having this problem sporadically, I was altering the stroke and wasn't aware that is what affected my cutpaths!
HOPE THIS HELPS YOU!