Don't think cable length is the cause. Anyway I see only one BOB on the photo and presumed you use Mach3.
Actually did you test all drivers set to "active low"? As far as I understand you have Y and A coupled as master and slave. Wrong polarity might make them "rough" as they need to move in sync while the others may also need low trigger but do not show rough movement because they are single. ??Hmm.