The springs are supposed to be a 1.8in drop. I have lowered other cars before and they were a similar story as your BMW, the spring only needed compressed a little bit for it to work out.How much lower are the springs supposed to be? Are you using dampers that will work with a lowering spring? Most likely the strut is too long. This will be a problem if you ever extend the damper enough to unseat the spring from the perch. Who knows how it will come back down. Every time you jack the car up you will have to re-seat it. Not a great idea in my opinion. Also check to make sure the upper strut mount and perch are installed correctly.
The H&R sport springs on my BMW are supposed to drop the car 1.5". When I installed them with Bilstein sport dampers, the spring had to be compressed about an inch to fit the spring hat and strut mount.