I just ran into the same problem.  After recording several demos over the past few days, with no problem, many of my mouse clicks (and resulting screen shots) are no longer being recorded in automatic mode.

I have been looking for the "preferences" file, so that I could delete it.  But, I can't seem to find one.  Is there a chance, if I haven't set any preferences, that I don't have one?

I'm on Windows 7 and looked in subdirectories of:

    C:\Users\<MyName>\AppData\Local\Adobe\Captivate 5\

Thanks for the tips.  I cleared my cache, renamed the "Captivate 5" folder and even shut down and rebooted my system.  None of this seems to help.  I must have reset a parameter that I'm not catching.  When I do something as simple as (mouse clicking each one):

  Start → All Programs → Accessories → System Tools → System Information  

All I get in the resulting file is a frame with the click on "Start" and then the the next frame is the System Information window (none of the clicks in-between). 

With the System Information window up, I expand each of the left categories by clicking the "+" to the left, but all I see in my resulting Captivate project is the screen that results after all three have been expanded (not each individual expansion).

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Update:  This appears to be related to the fact that I'm trying to capture from a remote desktop.  After adjusting my settings, and trying a few other tests with a co-worker, I found that the lack of screen captures only happens on this remote desktop.  The odd thing is that I hear the Captivate-initiated mouse-click, so I know Captivate is aware of this activity.  It's just not saving all of these mouse click screens.

I've done a couple of things since my last note.  First, I always hit the "Print Screen" button if there's a screen I want to make sure doesn't get lost.  Second, I updated from Adobe Captivate 5.0 to 5.5. 

My method of hitting "Print Screen" so many times adds some edit time, since I frequently get the screen captured more than once.  But, as I mentioned in my note above, this was primarily happening when I used a Remote Desktop. 

Two other things...  First, with the Remote Desktop, even if a screen wasn't missing, sometimes Captivate would capture before the screen finished refreshing, which also made my manual captures more useable.  Second, I upgraded to Adobe Captivate 5.5 about half-way through this project (which consisted of about 40 short demos).  I seemed to have fewer problems with the updated software.  But, I kept performing the manual screen capture because it seemed easier to edit out the duplicate screens than to get an entire demo captured, only to find a screen was missing (or incomplete).

Resoled by Pallavi from Adobe Helpline:

goto Edit menu >> preference >> recording >> settings >> automatic user FMR for:

uncheck Drag and Drop Action and Mouse Wheel Action

thats it