Do you have the "track splitting" feature enabled? If not, you have to manually end the recording. With track splitting enabled, MJ will detect the silence and end the track.
The time setting for the track is strictly an aid for the automatic track splitting feature and it's there to prevent the track from ending too soon, like during a quiet section of classical or jazz music.
I can help you set up the parameters if you describe what you're trying to do. If I guess correctly, you want to record an entire side of a cassette (with multiple songs on it) into one track in Media Jukebox and have MJ stop recording at the end of the side. You should be able to do this by enabling track splitting, and setting the duration of the one track to the entire length of the side, plus a few seconds since the start time is inexact.
Hope that helps,
John T.
JRiver, Inc.