I’ve used audio from the line-out on the computer for all of my computer use and I haven’t had this problem.  My guess is that there is something about using the internal soundcard that is causing this problem.  When you used USB speakers, you weren’t using the internal sound card, the USB speakers were the soundcard.  If you want to use the speakers you are using without this problem, you may be able to solve the problem with a USB sound card and plugging the speakers into the output of that sound card.  You can get a very cheap sound card to test this with.  I believe you can get them for less than ten U.S. dollars.