Thank you guys! Moving the clips to a new sequence with 1024x576p PAR1.0 makes it look like it should. There was some jagged lines going on that has now dissapeared. Scaling artifacts?
Just to make sure everything is set up correct (and I suspect you'r a little interested as well

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Source DVD (I always own the DVDs I edit with ;P)
PAL
16:9
720x576i
(PAR != 1)
25 fps
OK! so I resize/deinterlace with Avisynth
1024x576p
PAR = 1
-> 16:9
25 fps
New sequence settings
1024x576p
PAR = 1
25fps
Old sequence settings
720x576p
PAR = 1.45... !
25fps
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There you have it, I didn't notice because as you said the PAR streched the image to fit the preview.
I feel kind of stupid to make that mistake and not notice it before the AMV is more or less completed. It was an easy fix though.