Phase loss in a PowerFlex drive is only sensed via monitoring of the DC bus ripple. It really means "excessive DC bus ripple", but 99% of the time the only thing that causes that (other than issues that would be picked up by other protection functions) is the loss of an input phase. In fact if your load is very low (<50% of drive rating), the DC bus may hold up fine even with one phase missing. That's why you can use any PowerFlex drive as a phase converter without any special programming.
Why this only happens when you are changing direction or jogging is a real mystery though. More details of exactly what you are doing and how you are doing it might lead to an explanation.