Apparatus, methods, and articles of manufacture for encoding a compressed media stream are disclosed. Example method of watermarking a digital media signal disclosed herein include copying compressed audio packets associated with an audio stream included in a transport stream of the digital media signal into respective frames of compressed audio data to be watermarked to include media identification information. Such example methods can also include determining whether a composition of the transport stream has changed during copying of the compressed audio packets into the respective frames of the compressed audio data. Such example methods can further include, if the composition of the transport stream has changed, writing the frames of the compressed audio data to an output stream corresponding to the digital media signal without applying a watermark to the frames of the compressed audio data.