I take it you got the board OK then
Notes on zCode are here (read them!)
http://www.odysseypaintball.com/zcode.html
Check that you have plugged the board up correctly. The harness leads need to be the right way up and going to the right set of pins. Compare what you've got against the photocopy I stapled to the packing slip.
Next, it sounds like your batteries are on their way out. Use the stock 6xAA setup, and use fresh non-rechargable batteries.
To solve the Red/Green lights mystery:
Flashing red/green lights means EITHER
- the board has detected a jam (the hopper will spin three times, then stop and give you red/green)
- the board has detected low current (low battery)