I don't know if there is a problem, but the middle burner flame is definitely different. I ordered a set of burners for my Silver and I noticed they were different than the OEM burners...fewer gas jets spaced further apart, but larger jets. And the crossover tube had holes that were punched rather than slots that were stamped from the OEM. The material also seemed thinner. There was nothing wrong with my Weber burners so I cleaned all the jets and re-used them. The point of this is, do you have a mismatched burner set? Is the middle burner jetted the same as the outer burners?
I really hesitate to suggest this because you have swapped burners, but that's all I got. Good luck! And if you ultimately resolve this, please, let us know. I'm stumped.
EDIT: I'm going 'way out on a limb here, but the closest thing I can relate this to in my experience is like adjusting an oxy-acetylene flame. That's what this reminds me of, where you go from an carbon-rich (soft) flame to a neutral flame, and you have that different colored flame cone. I may very well be wrong, but my instinct is that it is rich, or improperly mixed. That's my best guess, but I'd sure like to know.