If I change Runed Ornate Rubies to Runed Crimson Spinels, the whole gearing strategy changes. I would expect no changes to occur since they give the same +12 spell damage.
snapshot id: 64558da8da33490b84ffcac65f08e040
Could you give me a second snapshot of the other result that you are getting?
Sometimes when you start locking gems, it can arrive at a slightly different solution. The difference should be negligible though – impossible to detect a difference in-game.