Lin, no one has suggested so far, but a systemic like Thiomyl will nip this situation quite effectivly. I have been successful on too many advanced cases to discount this treatment. It's a wetable powder that keeps in a spray bottle and I use it whenever I suspect something awry in my terrarium I got it from Thiomyl OSG23: Camp Lot A Noise Tropicals
i have a similar neglected phal, that has that same black spot in the base, yet the plant seems to continue growing normally. The roots exposed to air in the surface of the pot, became black. I cut one of the roots, and looking at the cross section, the outer layer of the root is black and very hard, not mushy or rotten, while the center of the roots remains green and healthy what kind of condition is this?
Dark brown roots often indicate exposure to too high a concentration of chemicals - either the fertilizer is too strong, or the mineral buildup is too great, and flushing is desperately needed.
Black, on the other hand, is more likely to be a mold, or bacterial, or fungal infection. I have seen the velamen of the roots get infected with a mold, and it eventually suffocates the root and kills it. Try a Physan or bleach treatment.