If you're working on a very complex song with a lot of CPU intensive effects then it's possible that your computer's not up to the job, but that wouldn't be my first guess. Especially since the audio is fading away until you reselect your interface.
Since you say it starts happening after a few minutes, not whenever you try to play the track or something like that, I'd suspect that it's an issue with your hardware or the driver for it.
Just to make sure it's not your computer running out of resources though, watch the little DSP meter at the bottom of the screen in Reason. It has a maximum of 9 tiny bars, and if it gets up that high then your computer will be struggling and will probably pop up a window saying that it's too slow to play back the song. In that case you have to get it started again by pressing Play or Stop before you'll get any more sound out of it.
If the DSP meter is staying low or in the middle somewhere though, you can pretty much rule out lack of processing power, and I'd focus on an issue with your interface. Maybe try disconnecting it for a while to see if you have any issues without it.