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Thruster motor suttering / jerky

my rov had its pix4 and ESC (Hobbywing 3-6s) die on me. So i got the new parts in and started to replace them. I had to flash the ESC with a firmware. When checked with the other esc it was using Flycolour Raptor 390 20A, So I loaded that in and discovered that it does not have bidirectional capabilities. So I then made changes accordingly following the same setup as the working esc. But when i tried to throttle forward my new esc would cause the thruster to jerk badly. where did I go wrong? I am using BLHeliSuit 16.7.14.9.0.1
i am using SILABS BLHeli Bootloader (4way-if)
i am using an Arduino Nano w/ATmega 328 for interface
Need your kind guidance and advise please.

To me it sounds like a sync issue from the input signal. Can you check if the signal you send is steady and correct? Maybe with an oscilloscope?
Did you calibrate the esc after the change? full throttle forward and full throttle backward.
It could be you are passing the 2000ms so the esc is going full throttle forward first and full throttle backward second time slot.
All this depends obviously on the kind of jerking it does. Is it vibrating, changing speeds but same direction, is it high power jerks or you can hold it with your fingertip?

Thank you for the advise Robin,
Unfortunately the technician who supplied me the rov was giving me the wrong information. The wrong firmware to be flashed into the esc and thats why it could not sync. it works well now.