During Compile, the Quick mode will re-multiplex an MPEG file in place. This parallel process saves some time and disk space, but it is also much more prone to errors. If the MPG file has different mux rate than DVD the compile process may not get audio data fast enough which will result in cut audio. For best input compatibility, it is recommended to demultiplex the file or use Elementary streams. You can also change the behaviour of Quick mode in Project Properties - Options.