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Your project settings clearly don't appear to match your video specs.
How are you getting a 640x424 video from that camera?
Steve, good question! It wasn't easy to find in the manual. 640x424 (3:2) is the default setting. Go figure! It's one of 3 settings all of which record at 24 fps. Of the other two, one is even more inexplicable: 320x216 (3:2). But the other one SHOULD BE the default: 1280x720 (16:9). There's a DSLR preset in PE9 that looks like an exact match. Thanks!
According to http://www.nikonusa.com/Nikon-Products/Product/Digital-SLR-Cameras/25446/D90.html#tab-Prod uctDetail-ProductTabs-TechSpecs that rather odd size is what they call VGA resolution
Of course, using a $100 consumer program to edit video from a $900 (msrp) camera does leave a few options off the table, when it comes to adjusting a project to match the video
If the OP really wants to edit VGA video instead of the HD 1280x720 24fps video the camera will produce, Premiere Pro allows custom projects
I wish that's all it cost! Actually, the D90 isn't what I'd nornally use for video since it doesn't have autofocus (in video mode) and it's mono. It's also a bit on the bulky and fragile side for casul family videos. I used it at Christmas because my camcorder battery went dead. In any event, I DON'T want to edit VGA video. That's what the camera was set to and I didn't realize it. So the $100 consumer program should be fine.