It is obviously not just a matter of replacing the cables, as you have just found.
Do you understand what I said in my earlier post about wiring loops and have you checked for and eliminated them ?
Have you tried bypassing the breakout board as suggested by Chris ?
Have you tried another PC to eliminate possible pp problems ?
Your earlier statement may perhaps be true "It's now left me with 2 possablities, it's either the bob or mach3". I think we all know it is not Mach3 so junk your BoB and replace it with a known good one, perhaps from CNC4PC
http://www.cnc4pc.com/Store/osc/advanced_search_result.php?keywords=breakout+board&x=21&y=9This is the direction I would take.
Tweakie.