Hi, Dave
I was saying run the Gecko's direct from the computer P-port, To eliminate the BOB interaction for a test.
Another thought, Are the Y axis wires routed in the same manner as your other axises and away from high/current power wires.
Are all your steppers the same and current set resistors the same, Yellow Led's on the Geckos lighting up the same.
Have you adjusted the midband adjustment's also, per the Gecko's manual, Checked all the connections..
Hood, I've always run my Gecko's direct to P-Port in testing, Don't recall any issues ether, Hi or Low.
Thanks, Chip