Run the gcode generated through GPX:
http://www.thingiverse.com/thing:81425Just need to drag and drop and it converts it to a proper x3g file for the Rep2.
I don't recall if the default start/end code for slic3r was compatible with Replicators, I don't believe it was.
Whpthomas also made custom profiles for slic3r that are makerbot compatible here:
Never tried Cura, but I believe you'd just need to make sure the start/end gcode is correct and then convert them with GPX the same way.