Hey Harko - I think I was the first person to protype the 5th Gen Brackets - what you are describing is not uncommon. If you have a large gap, you are likely to have an issue, but even installed correctly, there is a
tinnny difference in the gap size. My hood still closes safely, and it has settled to the point of being unnoticeable to me. I am not sure if anyone has gotten it to sit perfectly flush, and I am not sure if we know why. As far as I can tell, it really doesn't come into contact with anything other than a very small corner of the plastic trim between the hood and windshield. I believe the contact is only on the drivers side of the hood.
Do you have any photos of the gap? This is what mine looks like - if you go to Flickr you can zoom in. Very minimal. But defiantly something I noticed immediately when I installed them. Either the little trimming I did, or the weight just settled. Never look twice now.
IMG_2507.jpg by
tConrad81, on Flickr