Sound Blaster Live 5.1 is an audio card, which you probably don't use anymore, since you replaced you computer, with all-in-one motherboard. Speaker system must be one of GigaWorks or Inspire, but you didn't provide that information.
Since you wrote this started happening from the thime you replaced your PC, I will share what I experienced myself, see if one of these applies to you.
- Speakers are connected with Digital Cable (SP-DIF or the likes) and when no sound is playing, speakers "go to sleep". When sound starts to play again (any system-sound, for example Windows bleep when browsing internet, in my case) speakers restart with big whomph (my logitech 5500 does that, exactly as you wrote, half-a-second thump).
- Your sound driver / application is set to "energy saving" or whatever, that causes it to disconnect it's outputs when no sound plays for certain amount of time. Try finding and changing that setting. I can't provide exact step, because I have no ubuntu desktop and can't know how driver / application looks like. I will provide, however, screenshot of my DELL computer's driver app. My system isn't english, though. Note, that when this is turned on, I also get a quiet thump in my headphones, but not as alarming as the one from Logitech Z-5500 and my desktop PC.