Was the red naphtha cloudy? Did you shake it too vigorously?
Yellow naphtha is not necessarily a bad thing.
Also, have you checked the MSDS for your naphtha? Some brands contain significant amounts of aromatics which will pull darker.
Natural materials such as root bark will exhibit variability of composition - perhaps yours has significant amounts of a red substance?
“There is a way of manipulating matter and energy so as to produce what modern scientists call 'a field of force'. The field acts on the observer and puts him in a privileged position vis-à-vis the universe. From this position he has access to the realities which are ordinarily hidden from us by time and space, matter and energy. This is what we call the Great Work."
― Jacques Bergier, quoting Fulcanelli