I'm glad RacerX finally mentioned to do all adjustments in small increments. Part of your body's problem could be that 5 or 6 cm is actually a huge change in your position on the bike. Raise it back to within a cm or so of it's original height and go from there.

Everyone else is pretty much spot on as far as using fit calculators. I lowered my saddle a little after using one, but no where near what it suggested. I'll give myself a little time to get used to it and go from there. Bike fit is a pain sometimes, literally. It takes a long time and a willingness to be very patient. Good luck!