This is my quarter-assed guess; worth half as much as a half-assed guess.
I think the problem could be that the probe puts logic level signals through a relay that is really intended for power circuits. What happens is that the contacts oxidize and do not make good contact and the logic level voltage does not have enough oomph to drive through the oxidation. Relays with gold plated contacts are needed for reliable logic level conductance.
Try carefully treating the relay with contact cleaner.