What kind of lowering spring?
Without seeing it, so take this all with a massive grain of salt: I presume your lowering springs are shorter than the stock springs, combine that with the raceseng plates which are lower profile than the OE top hats and now you have a gap between the spring and the top hat when you are in the air, the Koni's don't have anything to do with it, you'd have the same issue if you had the stock damper + lowering spring + raceseng camber plates.
Easiest solution would be to have a 'taller' spring perch made to match how 'tall' the OE top hat is. Or you could just set it down on the ground and go drive it, odds are nothing bad will happen if this is truly what's going on.
The joys of combining modifications.
