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First, I'd suggest performing what I call a simple "sanity check". This should reveal to you whether the issue is with Captivate generically or if it's just that Captivate has issues with this one application.
So try this. Open Captivate and minimize all apps. Then record dragging an icon from one location to another on your desktop. If Captivate doesn't record that properly, you have a Captivate issue. If it does, you know it's an issue with the application and the way it interacts with Captivate. In that case you need to consider other avenues. Perhaps use something like Camtasia Studio or Jing to capture, save as SWF and drop it where you need it in Captivate.
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Captivate 3 is terrible at this kind of capture, so you might want to fake it a bit. Turn off Full Motion capture. Then press Print Screen before you start dragging. Then drag a bit and Print Screen, drag a bit more and Print Screen, etc. Then set each 'stop motion' slide to, oh, 0.1 or 0.2 secs. To your viewer, you appear to be dragging, but . . .
I think it's better to think about Captivate as less like a movie and more like a flip book. You can create the impression of movement with a series of slides set to very short timing. Let me know if that solves your problem.
E-Learning Developer/Captivate Coach