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From my experience, the full motion recording (at least in Captivate 2) is pretty finicky. I'm guessing the problem becomes more pronounced as you increase the dimensions of the screen you're capturing, since I capture at 1000x700 and it usually takes me half a dozen tries to get something "good enough".
Captivate 2 also seems to have a thing for grabbing the application one or two pixels larger/smaller than it should during FMV capture, since all my animations visibly "shift" in size by a pixel or two and are thus blurry when they play back. I'm too lazy to implement a workaround, so again, I just accept that "it's good enough".
I dunno if full motion recording is any better in Captivate 3, but try to use it as little as possible in Captivate 2...
It occurred to me that the herky-jerky nature of FMV recordings may also have to do with the frame rate of your Captivate file (as set in the Project preferences).
I think the default is 12 frames per second (at least, that's what all my movies are at and I don't remember changing that). Captivate probably also uses that value when capturing an FMV.
A mere 12 FPS seems mighty slow for a "full motion" recording, so you could always try upping that value to 24 or more and see if that helps.
Captivate 3 is, in fact, much better at handling full-motion capture than is version 1 or 2, but it doesn't sound to me like a "version problem" in any case. Personally, I wouldn't worry about the frame rate - leave it at the default - as changing it is unlikely to help, and quite likely will add a confusion factor to your trouble-shooting efforts.
I agree with your thinking that it acts like a resource problem. To eliminate this, you might want to open MSCONFIG ...
(Start menu > Run > (type) MSCONFIG > click OK)
... and go to the "StartUp" tab, de-select all startup items in the list, then reboot and try again. (Don't forget to reinstate the startup items you actually want when you are done trouble-shooting).
I've seen this same behavior - kind of - caused by a difference in alignment of the mouse-pointer (Demo mode recording) on the slide prior to the full-motion (FM), and the actual position when the FM starts. I never have the problem described earlier, and I never settle for "close enough". Here is how I handle any "jerking" when the FM begins:
On the slide before the drag-and-drop operation actually begins, I carefully move the cursor to the exact position that the drag should start. At that point, I make sure the cursor doesn't move while I take a manual capture of the cursor and background in that position. Then I begin the FM capture ... being careful not to move the cursor until aftermy left-click forces the full-motion capture to begin. This takes a little practice, but will eliminate the "jerk" that many see when FM begins.
Hope this is helpful.