Random Rythmic knocking in motors

Ive been getting this rhythmic knocking noise in my stepper motors randomly it'll be fine one moment, I step away for a little bit then I get this knocking whenever i jog or run a program, It'll also just go away randomly. Its causing the motors to stall if the feed rate is to fast (over 11in/ min) losing steps and ruining my work piece. When I first installed LinuxCNC onto a dedicated computer it was working fine then an update happened and it started the knocking. I am perplexed to what is happening and my boss has is computer hooked up to the same machine but he runs Mach3 and no knocking which leads me to believe that is something in the controller software. I rather not have to wipe everything and start over.

Any advice?

Thanks

I cant remember what exactly but I just clicked on the update button and updated I didn't really think much about it.

I would re-run the latency test to see if its gotten worse
Do you get any error messages from LinuxCNC?