I seem to recall a short while ago someone asking for advice on a mysterious ‘knocking’ sound emanating from the headstock of a Colchester lathe they had recently purchased. I don’t think the issue was satisfactorily resolved and such is the nature of this site, I cannot find the original thread. However, I did find this on the Lathes.co.uk website:-

“Mounted on a large adjustable plate inside the headstock end of the stand, the motor pulley was arranged to take either a wide flat belt or double V-belts. Although efficient, the twin V-belt drive can cause problems and, should the geared headstock on any V-belt drive Colchester make a knocking, rattling or rumbling sound, the cause may not be worn gears or bearings but unequal-length drive belts “fighting” each other. To check, try running on one belt to see if the headstock runs more smoothly; if it does, fit a second belt, run a chalk line across the two, start the machine……..”

As far as I can recall this reason was not raised as a possible explanation for the knocking sound, so perhaps this could have been the cause of the OP’s problem?