Delightfully simple:

1) Go to properties for the repeating section (right click it's bottom tab->
repeating section properties)
2) Display tab -> Conditional formatting
3) Add a new conditional formatting rule
4) Select if "the expression" is true
5) add this as your expression:  
    position() mod 2 = 0
6) Choose the background color near the bottom of the dialog and hit OK

This will format the even numbered instances with the color you want... if
you want to do the odd ones, this is the expression:
position() mod 2 = 1

Enjoy!