try Flashprint - it's what I've switched to for my rep pro clone.
http://www.flashforge.com/flashprint/
So much better than makerware and so far the on;y other slicer i've successfully done dual; extrusion with other than makerware.
But flash print is way way better and easier to use than flashprint :-)
Also chek com port baud speeds.
you want 115200 as the set speed.

New makerware doesn't really talk to older printers.
The fact that the older machines are infinitely better then the current models, probably has something to do with it :-)

Benchy lol
hate that boat.
Print something useful :-)