I've taken quite a challenge on here in that I'm trying to learn both Sonar 4 PE and GPO at the same time. Don't know much about either one yet, but working on it.
I've been setting up in Sonar and recording in the sequencer and every once in a while it would hiccup and stop for a second or two and then get on with it. Sometimes it would be during recording and sometimes it would be during playback. When I tried using Cubasis this didn't happen. I kept scratching my head for a while because I really prefer Sonar 4 to Cubase anything and finally last saturday I happened to be looking directly at the display (Sonay VAIO 2.66 gig P4 with a gig of ram) when it happened and I noticed out of the corner of my eye that down at the bottom left hand side of the track view window it said "automatic saving" and...BINGO! That's what the problem was. When I had originally installed Sonar I had been going thru all the menus and when I found auto save I thought wow, just like in Wordperfect, so I set it the same, ie, for 5 minutes or 5 changes. In Wordperfect it happens un-noticeably but in Sonar it takes 1 to 2 seconds and disrupts everything else. So I put a zero in both boxes and now Sonar works rock solid and I will train myself to simply use Control+S whenever I do something and get to a place where I want to save it again.
So if you are having strange stoppages, check the automatic save function and reset it if need be.