Funny thing - early yesterday morning I was tracking out a show I recorded late last week. So as to not disturb anyone, I listened using earbuds plugged into my computer speakers.
While listening to various pars of the show, I suddenly heard the right channel slowly fade out and disappear. My first reaction was to think the recording was messed up. Turns out, once I reinserted the connector plug (3.5mm), everything was fine.
Maybe the op just had a dirty cable connection.