OK, for me a downgrade to 10.6.7 worked
I did solve it but I am afraid not many can or want to copy that. I hope though that it helps to find the glitch. My story isn't very scientific because I moved to another country when the troubles started and I didn't pay attention at first, but ok:
Since 2008 I have a iMac dedicated to music (iTunes) and tv (eyeTV). The sound is hooked into the hifi with a fire wire connection to an audiofire2 DAC. I only play files that I ripped of my cd's in Apple loss-less. I don't download, I don't listen to streams. This has worked fine until fall 2012, when I did one of the recommended system updates (I think 10.6.8, but it might have been a month earlier). Since then I experienced glitches when the soundtrack became silent or very soft. As I listen a lot to classical music this is killing. One second of complete silence and than the music resumes with a snap. Unbearable. Strange enough, and I have not seen that reported but I think it is important: when playing over the internal speakers of my iMac, there are no problems/glitches. I therefore think the problem is in a driver.
Over a year or so I tried several things (re installing etc) when I had some spare time (I moved remember). A few months ago I made a big effort to go back to a version of june 2012. I erased the computer and I am running now iOS 10.6.7 and iTunes 10.6.3. My music library was of course copied. (In case I solved it by pure luck I add that I changed the internal battery 3V as well. No idea if disconnecting that for a few seconds can do anything).
The whole old system now works perfectly again and has been stable for 3 months. But I wouldn't mind to be able to update my system, which of course is out of the question now.
I hope it helps some of you, but mostly that it helps the Apple engineers TO START SOLVING THIS
Tim