The color of the roots can be affected by the drying process. Even roots that were dried properly will be brown on the outside, but should still be yellow in the middle. If it's not yellow in the middle when dry, the roots could have been dried to fast (causing discoloration), or they may have been old and sitting around for awhile. Either of those two factors would also affect alkaloid content of the roots and cause variation in medicinal quality. The alkaloid content of the roots is also variable based on how and where they were grown, i.e. amount of sun, soil composition and pH. Based on research trials, roots that recieve more sun tend to have higher concentrations of medicinally active compounds, resulting from stress on the plant from excess sun. Those are the most likely reasons for the differences in product and medicinal potency.
I think the best way to take goldenseal is by extract. If you are making your own extract, or other medicines, I would recommend using fresh roots rather than dried.
Rural Action Forestry