Abstract: An encoder system includes an internal counter (PTS or presentation time stamp counter). The counter provides information which enables the encoder system to resynchronize itself in the event synchronization with the video input stream is lost. Preferably, the counter is implemented in software. The encoder system also include a comparator (preferably implemented in software). The comparator is able to determine if particular regions of the input video stream have been captured at an expected time according to the internal counter within a predetermined error window by comparing the actual capture time with the expected capture time. In general, if the encoder system is synchronized with the incoming video stream, each successive blanking or active region will be captured at its expected time according to the internal counter within a predetermined error window. In this event, the timing of the various modules of the encoder system (e.g., preprocessing, spatial encoding, etc.