Read Bill Hunt on a file type as WRAPPER http://forums.adobe.com/thread/440037
What is a CODEC... a Primer http://forums.adobe.com/thread/546811
What CODEC is INSIDE that file? http://forums.adobe.com/thread/440037
Report back with the codec details of your file, use the programs below... a screen shot works well to SHOW people what you are doing
After importing the "bad" video, and before doing any work, does your timeline have a red line over it?
If yes, your project and video do not match... see above for how to determine the details of your video
you need to give us a little more info about the video which include video format, size etc.
camera's model is important as different models have different specs.
It sounds like you might have mixed Frame Rate, say with NTSC 29.97 FPS and PAL 25 FPS.
That additional info asked for, plus the Project Preset that you chose, will likely tell the story.