when is the last time you flushed you s/h ?And how long do you flush dosent really sound like that is it but a really good flush would not hurt .....I had a that happen a bit at first with mine but just the roots at the very top of the container.
I flush every week now and lol very very well I put the few I have in the bath tub and use the shower head on a hose to realy flush and tip the pots to get as much water out as I can and flush again.THen I leave them in the tub and let the shower run up to 10 mins ...a little ocd but it helps.
I also started using the plastic folgers coffe cans for s/h pots .They are red colored and you can not see through them but they seem to keep algae out for the same reason.
I would try some bayer three in one mixed to directions ..5 1/4 tabelspoons per gal and drench them with it letting s/h pot get filled with it and leat it sit for about a hour then drain and fill with fresh water ...I did not flush after draining just filled with plain water.The next day I flushed well and refillied with fert solution I use.
No dead roots since for me
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MT-Phal 
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