A computing system detects a channel multi-match with non-matching programs, based on fingerprint-based ACR analysis of digital fingerprint data representing a channel rendered by a content presentation device. The system then responsively performs disambiguation based at least in part on detecting an earlier single-channel match and/or a later single-channel match, the disambiguation establishing that the channel rendered by the content presentation device is the single known channel. And based on the disambiguation, the system then uses the single known channel as a basis for carrying out of at least one channel-specific operation, such as recording audience-measurement data and/or invoking dynamic content modification.