If you're talking about springs "creaking", I have the same issue on some of the keys on my HHKB. It seems to be very random, and I haven't found any good fix for this. I remember someone talking about lubing the springs with dry lube, but I haven't tried that myself. I would be careful lubing the springs regardless as it can mess up the capacitance.
Not sure about the BKE inconsistency, but I've heard some say the domes need time to break in.