An endpoint or other communication device of a communication system includes a clock recovery module. The communication device is operative as a slave device relative to another communication device that is operative as a master device. The clock recovery module comprises a clock recovery loop configured to control a slave clock frequency of the slave device so as to synchronize the slave clock frequency with a master clock frequency of the master device. The clock recovery loop utilizes a frequency error estimator implemented as a maximum-likelihood estimator with slope fitting based on a sequence of arrival timestamps, and a loop filter implemented as a series combination of an adaptive-bandwidth filter and a proportional-integral controller. The clock recovery module may further comprise a discontinuity detector configured to detect a discontinuity in delays of respective timing messages, and a loop controller operative to place the clock recovery loop in a particular state responsive to detection of the discontinuity.