Hi biko30,
I had the same problem with mine, just assembled this past weekend. I used the rubber handle of my hammer to (gently!) seat the tweeter, working around the circumference. I couldn't push hard enough with my thumbs! It's pretty well flush now but looked like yours at first. The woofer seems to flex a bit and when tightened down kind of conforms to the tweeter. I'm a first time builder though, I'm sure there's more experienced advice on here.
Good luck!
Tom