Hey Kal,
if can you eliminate a loose milling bit in the collet, in theory three possible reasons could be the cause, a loose ball screw coupler, missing steps on the stepper (possibly by a bad cable connection) or a software bug. The latter seems not to be the case since you said it does happen at random, also software bugs mostly are reproducible, and your issue seems not.
A loose coupling between stepper and ball screw is possible since steel expands and shrinks with changing temperatures. Even cooling down during shipping and warming up during reception and assembly can be a cause of shrinkage and stretching, and thus of screw connections that become loose. Also heat and thus expansion could arise after a certain period of time after the start of a work process.
A loose coupler could behave like losing steps in one direction.
I would check if this screw connection has become loose. For this I would shut the controller down and power it off (or disconnect the Z stepper) and then try to move the Z slider up and down and try to listen to the noise and to find out if there is play.
If the coupler is slipping, there is a video on how to fix the screw again: Support: How to tighten the coupler on the ball screw. It shows on X or Y Axes but with Z Axis it is similar, with the difference that the coupler is better accessible, as can be seen on this video. On Z Axis, the ball screw does not need to be removed in order to fix coupler screw.
This is however in theory. It is always a good idea to first contact support@onefinitycnc.com.