When you breed two pokemon, 3 IVs will be choosen from the parents and inherited.

Using the Destiny Knot increases the number 3 to 5 to be inherited.

So even if you do have 6 perfect IVs with both, there's no guarantee it'll choose the perfect IVs for BOTH.

For example, let's say your baby will inherit all stats but ATK.

Whose HP will he inherit from? You have 50% of getting a perfect one here (since only 1 parent has it perfect).

Whose DEF will he inherit from? Again, 50% chance.

Etc

The faster way to breed would be to pick Dittos with a perfect IV in a stat your other parent also has maxed, so you'll generate babies who'll become parents BOTH with perfect IV in that particular stat.

So if you can get your 3 perfect IV Male X breed with a Ditto (use power items, or Destiny Knot and get lucky) and get a new 3 IV perfect Female X who stats overlap with the male one, there's a high chance you'll get those stats inherited.

With this you have very high chances of getting new babies with perfect HP and ATK since both parents have it, and by this time you need to get lucky and achieve a new perfect IV in another stat. Once you do, use this new one as parent, and now you got even more chances of inheriting that stat until you DO get a new baby, of the opposite gender, with that perfect stat.

By then you should have 2 babies of each gender with 3~4 perfect IVs. Repeat until 5, eventually 6.

You can do the way you're doing, but you'll need to be lucky for all 5 stats to be chosen correctly (from the perfect parents), and that might take one egg... or 200.

This way I just explained is a more guaranteed way, takes more work, but rely less on luck.

Also, by using the Destiny Knot when both parents don't have the same perfect IV on each stat is... really pushing your luck imo.

Because you're locking your babies into the non-perfect stat of a parent instead of getting a new one.

Let's see, if my probability math is right, you should have...

50% of getting the right HP (total: 50%)

50% of getting the right ATK (total: 25%)

50% of getting the right DEF (total: 12.5%)

50% of getting the right SPATK (total: 6.25%)

50% of getting the right SPDEF (total: 3.125%)

50% of getting the right SPD (total: 1.5625%)

Oh man... good luck!

FC: 2552-1500-0922

Pokemon X, Trainer Name: Mimi