I had suspected that Repetier would pull the enable pins low.
Try this Simple Stepper Code which does not use any library.
If that does not work you will just have to delve into the innards of Repetier to see what it may do differently.
If it does work it says something about AccelStepper - but I don't know what 
I don't know if AccelStepper claims to work on a DUE or if it uses some resource that may conflict with one of the pins used on your board.
I'm assuming that your board can have a max of 3 x A4988s
I don't have a DUE.
...R