Alternators get a lot of stick, but they are very reliable in general, however depending on the design you will have a brush box at the end on the shaft or rings pushed over the shaft, these carry the brushes to the commutator for the want of a better word.
The brushes movements to contact the power source must be free in and out of the holder, sticking brushes are a well known fault.
As you have interfered with this area when fitting you smart charger I would revisit this and check. One of the quick checks we did in production of alternators when this happened was "wack the area near the brush holders" this was a controled wack not a 5lb hammer. If this sorted the issue we stripped out the brush box.
The other thing is alternators are not designed to be fitted with after market smart chargers, look in the small print of your smart charger, they opt out of all responsibility for their wrecking of the alternators. I have said this before on this forum, put you hand on the running alternator fitted with a smart charger under load, its well over the optimum safe running temperature. Fit a property designed one.
Hope this helps
Odysseus
Bav 38