Make sure everything is settled in (take her for a short spin) and the car is parked on even ground before measuring the ride height. I doubt very much there's anything wrong with the struts or shocks. Sounds like assembly error to me, if anything. If necessary, I'd pull them out, verify everything, follow the manufacturer recommendations to the "t" (I called them for better adjustment instructions when I installed mine, and I would NOT use an impact wrench), and very carefully put everything back together. My Koni's (with stock springs) ride like a dream.
P.S. If you haven't already, be sure you install the reinforcement plates when you reinstall.
2004 BMW 330i ZHP (52k miles), Jet Black with black leather, MFactory LSD (3.38) with Z4 cover, 18"x8.5" ET38 APEX Arc-8's (Anthracite) with 245/40 Michelin PSS', Koni Sports with factory springs and front and rear reinforcement plates, Shark Injector, Corsa TSE3 cat-back exhaust, TMS under-driven pulleys (water & steering), CDV delete, TMS CF strut brace, K&N CAI, GAS DISA rebuild, TMS pedals, Wheelskins steering wheel cover, roller tray center console, black-out grilles, and WeatherTech mats