We get this question from time to time and as the new Cookie from Flavour Art is fairly clear instead of amber colored I thought I would bring this up 
I have been told that with flavors without artificial coloring, the color we see is dependant on the order of ingrediants being mixed. The order of ingrediants affects the PH which in turn affects the color. Even though the ingredants are the very same as in say the last batch of the same flavor. The Ph does not affect the flavor of the flavoring, only the color. Most companies combat this by adding artificial coloring, this is why LorAnns Rootbeer is always the same color.
I have been told that with flavors without artificial coloring, the color we see is dependant on the order of ingrediants being mixed. The order of ingrediants affects the PH which in turn affects the color. Even though the ingredants are the very same as in say the last batch of the same flavor. The Ph does not affect the flavor of the flavoring, only the color. Most companies combat this by adding artificial coloring, this is why LorAnns Rootbeer is always the same color.