Undersensing of an evoked response during an automatically initiated search of the stimulation threshold in a stimulation channel of an IMD, e.g., the pacing threshold in a pacing channel of a pacing system, is minimized by repeating the search using the sense amplifier of the stimulation channel configured in bipolar and unipolar sensing configurations. A failure to sense an evoked response in the search in one sensing configuration can be confirmed, and stimulation energy set to a high output, if an evoked response is not sensed in an alternate sensing configuration or refuted if an evoked response is sensed in the alternate sensing configuration. If the failure is refuted, the alternate sensing configuration is employed until the next search.