By default, mencoder uses the first audio track of the input file; if there are several audio tracks it may not be the one you want.
You can try adding the option -alang en to both passes.
If this doesn’t work, you have to add -aid (ID), where (ID) is the audio ID of the track you want. What ID you need to set depends on the input format. For some formats the IDs are counted starting from 0 or 1, so you would have to use -aid 1 or -aid 2 to get the second audio track. For DVD video (VOB files) they start at 128, so you have to use -aid 129 for the second audio track.
(btw, if you don’t want to wait for the whole lengthy video to be encoded just to see if you have found the correct audio track, you can use the -ss and -endpos options to convert only a small part of the video, for example -ss 120 -endpos 20 to seek 120 seconds into the video and then encode 20 seconds only)
