Welcome to the forum.
First, what are the full specs. of the source footage?
What is the Sequence Preset and what color line do you have over the Clips?
Can you give us the full specs. of your computer, and especially the hard disk drives?
Last, you say that things work upon reboot, but over just a little time, things no longer work. What programs and processes load at bootup? Task Manager (on Windows) will give you most of those, and other utilities will go into much more detail.
Thank you for your prompt response. The tasks are attached. Other responses below:
BTW - my Encore will not work at all and I have reinstalled. It chokes on any file type I try to import. That's another story.
You have something seriously wrong... may be hardware or a bad install or conflicting or out of date drivers
Work through all of the steps (ideas) listed at http://forums.adobe.com/thread/459220?tstart=0
If your problem isn't fixed after you follow all of the steps, report back with ALL OF THE DETAILS asked for in the FINALLY section, the questions at the end of the troubleshooting link