Poor quality on movie after exporting it from Premiere Pro CS5.5

Hi!
As a part of my bachelor thesis in industrial engineering, I am making an animation that shows how different types of water turbines work.
The animation it self,  I've created in a program called Autodesk Inventor. From Inventor I get an uncompressed video. This video is usually not possible to open directly, but when I convert this with FreeMake video converter, it works
Conversion in FreeMake:
From:
RAWVIDEO
1280 * 720
16:9
663,554 Kbps
30 fps
To:
. Avi, mpeg4
1280 * 720
16:9
3283Kbps
30fps
The video looks great now, but now when i have finished editing the film in Adobe Premiere Pro CS5.5 and exported it, the lines are very blurred and bad. I've attached a picture showing what I mean. I have tried many different settings in Premiere, but i cannot get it any better.
The picture on the left is after exporting, the image on the right is after converting it in FreeMake Video Converter.
Have tried with the flicker removal, but with poor results.
Does anyone have any tips on what I can do?

Thank you for the warm welcome
Yes, the video from autodesk is uncompressed avi. These files are impossible to import in Premiere, and i cant open them in either VLC or WMPlayer.
After a conversion with FreeMake VideoConverter they are possible to import, and they look very good in VLC.
My Sequence settings are:
Editing mode: HDV 720p
Timebase: 29.97 frames/second
Video:
Frame size: 1280*720
Pixel Aspect ratio: Square Pixels (1.0)
Fields: No fields (progressive scan)
Display format: 30fps Drop-Frame Timecode
Audio:
Sample Rate 48000Hz
Display format: Audio samples
Video Previews
Preview File format: I-Frame Only MPEG
Codec: MPEG I-frame
With: 1280
Height: 720
Maximum bit depth and Maximum render quality is checked.
I have tried with a variety of export settings, but my current ones are:
Output:
Format: Quicktime
Video Codec: H.264
1280*720, 29,97 fps, Progressive, Quality 100, 48000Hz, Stereo, H.264
Aspect: Square Pixels
Render at maximum depth
Depth: 24bit
Use maximum render quality.
One thing I find quite strange is that i have to short clips at the beginning, which both seem fine.

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