One should have to do the Render only once, unless they make some change in the footage, i.e. a Title, an Effect, a Transition, and then should only have to re-Render just that section (see WAB - Work Area Bar). If you are doing a Render, and then upon restart of that Project, the Rendering is gone, there is another problem.
The link provided does go into a lot of good discussion on these particular files. There is a second similar thread, IIRC, with more comments.
Adobe admit there is a performance problem with mov. files from Canon 5D Mark II here in Australia and say a patch will becoming for CS4 ?
We use Premiere Pro 1.5.1 the first version capable of handling High definition codecs and an older Pentium 4 3.2 MHZ 800MHz FSB 2 Gb Ram and 500 Gb" C "and "D "Drives, it does a very good job and has done for 2.5 years in HD but, Canon's 5D mark II mov. has provided us with a problem on smooth timeline running to edit .
You need to render all the clips first and if you have say 40 min timeline it will take about 5 hours overnight and in the morning you have a very editable timeline.
All the files run smoothly with the exception of a minor glitch with the camera speed of 30fps say to a Project setting which may need to be changed if say you use Pal at 25fps or 29.97 fps if you export to tape which is the cheapest way of getting the video to say a Sony Bravia 46" and if you make a mistake with High Definiton , you will certainly see it.
Generally speaking the out put of the mov. files through Premier Pro 1.5.1 to tape is very professional, and the final result is stunning.
Note: There certainly are issues with jerky running on the timeline without a very good Quad or Duo Core computer.Unless the isssue is poor perforformnace from CS4.
Unfortunately Adobe's phone tech service in 4 years solved only one or two ploblems , they are close to incompetent as you can get.
Ps. The saving grace here is , is that premiere Pro is a marvellous product , but, the tech support is not a patch on Dell Computers who have often solved Adobe Portal support requests befor they have. it does not say much for the Technicians which is a great pity.
When Premiere is working properly it is first class ##################