IMO the most likely cause is a problem with the field wiring. To test for this, monitor the voltage at the controller between the zone terminal and common. When the problem occurs, if it’s a wiring issue, the voltage will remain high or increase slightly. If it’s a controller issue, it will dip low. (There is a small possibility of an intermittent partial short in the field wiring, in which case current measured at the zone terminal will increase.)
If you determine that it’s controller related, check the output voltage of the transformer. If that remains stable, try to get a warranty replacement. If it dips, check the voltage at the transformer input; there may be a problem with the outlet wiring, breaker feeding it, etc.