Could have been that the spring on the HKS was set up for Turbo and Not supercharger. You need a softer spring for supercharger because of the difference in PSI delivered between the two types of compressors. The softer spring will allow the BOV to release sooner whilst the turbo hard spring will hold more pressure. If your BOV had a turbo spring, which is most probably did, it would of been the cause for it not releasing fast enough and thus building too much pressure in the intake which in turn ends up sending the air back towards the compressor.
Very well documented problem on M3forum with guys trying different style of BOVs on their supercharged e46's. The TialQ50 which I had was known for being too loud, so guys installed harder springs to lower to volume of the choo choo, but then started getting compressor surge.
Anyway, glad you got it sorted.