Exporting Keynotes into Quicktime

I teach K-6 graders and I like to begin each lesson with a recorded lesson they watch on the computer in front of them and then we practice what I taught them in the presentation.  I was using Keynote, but it had problems with embedded videos at times.  I like to add embedded videos while I explain and show them what they are expected to do.  The audio would play but often the video would not. 
So I began recording the presentations and exporting them to Quicktime.  I didn't have a problem until this week.  Most worked fine, but two do not have the controls in the video.  By that I mean, when you mouse over the presentation, I would like students to be able to pause, rewind, rewatch, etc. as they need to but the controls are not showing up on the mouse over.
This is only happening on these two videos.  The rest work perfectly and I have tried multiple times.  I cannot find anything that is set differently.  The only difference is that these are made for 5th and 6th graders and are slightly longer than the other videos.
Has anyone experience with this?  Older discussions point to using paths that my version of Quicktime simply doesn't have and I am at a loss.
Thanks

Hi Patrick,
Thanks for the info. But I can not get any setting to come out looking widescreen. All settings come out square looking. I have tried every setting I can think of but all the QuickTime exported movies come looking like (i.e.: 800X854) more box than widescreen. I think it must be some setting I do not know about or some combination or possibly the capture setting (easy setup).
Thanks for your help.

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