OK - new USB 2.0 card did the trick. Spindle VFD isn't killing the SS and the mill seems much more responsive to jog commands (in fact it all seemed very sluggish via the old USB).

So, it seems like it's behaving like it did from parallel port control. Won't know for sure until I actually run a 4 hour job on it though

So old onboard USB  =  bad, new USB card = good

I too have had issues with some built in USB ports. Not on the SS but other devices like hard drives that transfer a lot of data. Glad you got it sorted.

I might have spoken too soon, tried running a job (aircuts only) and it failed after about 10 minutes. So I plugged a 5m USB extension cable into a PC on the other side of the shop and it ran fine for 4 hours straight.

So I swapped PCs, plugged the SS straight into the "other" PC and it failed as soon as the spindle started

Then I  plugged in the 5m extension cable and it worked. Turns out the 5m USB cable is heavily shielded and it actually has a USB hub in the plug at the end. So... I've swapped the PC's back and it seems to be working with the original PC and the 5m extension cable between the PC and SS (note that the SS and PC are still less than a meter from the spindle VFD).