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Minn, what version are you using?
Can you explain exactly what you mean by "the fields seem to not match up. They seen to be off a little"?
Do you get an effect like a comb or a rake has been run through the moving parts?
Or are you seeing something else?
Yes a comb through the moving parts is a great way to explain the effect. Any ideas?
Did you check it on a TV, not your computer monitor.
What you are seeing is a normal result of watching interlaced video on a progressive (non-interlaced) monitor.
If you intend for your finished video to be watched on a normal TV, then you don't need to do anything.
If you intend for your finished video to be watched on computer screens or hi-def TVs, then you should deinterlace your video before exporting it.