Sounds to me like someone was trying to take your saddle and was interrupted. Get a saddle leash or use an old bike chain to lock your saddle rails to the seatstays.

I say have the saddle at the correct height because as you noticed, your knees began hurting. After that, you may want to tilt the saddle slightly nose up to relieve pressure in the perineal area. While it sounds counter intuitive it actually allows your sitbones to take the pressure.