Possibly the audio sampling rate was not converted properly. Two things off the top of my head you could try:
Extract the MPEG1. To do this, first install ISOBuster. Select your drive or VCD file, click on the MPEGAV folder. Select all .dat files and right click, select "Extract but filter only M2F2 MPG Frames". Save it. Open TMPGEnc DVD Author and "Add File", specify your MPEG, TDA will offer to convert your audio to 48kHz, click OK. Author normally.
Extract the MPEG, then demux in TMPGEnc or bbMPEG. Open the MP2 (audio) in FFmpegGUI and convert the audio to AC3 or MP2 at 48kHz, and at a bitrate of 192 or above. Then input the elementary streams (m1v and the new mp2) to whatever authoring program you use. Rejig and IfoEdit (both free) can do it, also DVDauthorGUI, many others.