IV Stats/Judge Don't Match Up?

There is no contradiction. IVs are hidden values that add up to 31 into a stat at level 100. IVs are not your stats at level 1.

The red and blue highlights show which stats are boosted and lowered by the Pokémon's nature, they have nothing to do with IVs.

I suggest you read more about what IVs are, for example on Bulbapedia.

TL,DR: Trust the judge, it's not wrong. 6 best is perfect.

Full answer: You are confusing a pokemon's regular stats with its IVs. IVs are hidden values that boost your stats, but will have almost no effect at level 1. As both of those bulbasaurs get to higher level, you would start to see a difference between their stats. The #2 bulbasaur would end up having slightly higher special defence than the #1 bulbasaur, because of the difference in IVs.

You also have a nature creating a difference between the two bulbasaurs. The #1 bulbasaur has a neutral nature that does not raise or lower any stats, shown by the lack of any blue or red highlighting. the #2 bulbasaur has a nature that raises defense and lowers special attack, so as they increase in level that would cause a stat difference as well. When you reach end-game after the Championship, you'll be able to buy items that change nature to move the red and blue highlighting to boost stats you want and lower stats that don't matter to you.