Quoting David Baron <d_baron(a)012.net.il>il>:
Simply listening to music with mplayer or xmms running
through jack: I get
xruns approximately every 20 minutes--around the hour, 20min, 40min.
Not exact but +-2 second but around the third hour point.
Check your /etc/crontab and see if something there's the culprit. If
my suspicion is right you probably have an entry with 0,20,40 or */20
there.