You're doing it right, but it comes down to patience and luck. The destiny knot brings down 5/12 of the parents IVs. Basically like this
Male Female
HP HP
Att Att
Def Def
S.Att S.Att
S.Def S.Def
Speed Speed
It'll pick 5 stats of those 12. One from each stat type, ie: hp att def satt sdef speed, and will skip one all together. Since you keep getting 3 IVs from the parents, it just means that the offspring are randomly picking the less-than-perfect IVs of the parents instead of the perfect ones.
Edit: excuse the format of the male and female stat breakdown. The spaces are there when i type them, but when i post, it scrunches them and i frankly don't care to look in to why. You get the jest of it.