I would be very suspicious of the BOB. The design of the opto circuits on that board leave a lot to be desired, especially for servo systems that require much higher step rates than steppers. I had several C11s, and they all topped out at a very low step frequency, and badly distorted the signal. I was able to re-bias the optos and get them to run over 125kHz, but out of the box they completely stopped passing the step pulses at something well under 30kHz, due to improper opto biasing, and a strange pulse-shaping circuit they use. If you slow down your max speeds, and the problem goes away, that would be a good indication this could be the problem. If you can prove the BOB is at fault, I suspect you could get Arturo at CNC4PC to swap it out. He exchanged mine several times over a number of years, and finally swapped the C11 for a, IIRC, C25, which behaves much better.
Regards,
Ray L.