machine pulsing and missing steps

After changing to a 3rd generation board from ENGMATE I am having problems getting it to run.
On start up everything moves fine using the arrow keys on the pc keyboard. But when I try to run a file to cut the x and y move intermittent while the program runs fine on the pc. If I switch the board and stepper drivers off and back on it will eventually run as it should, missing some steps at the start. Sometimes this can take several attempts.

When it does run it has more than ample power with no stalling issues

https://youtu.be/-QPHHP79W8E