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Do you use the Morrowind Code Patch and Patch for Purists? If not, I recommend them. Together they are Morrowind's equivalent of the unofficial patches for Skyrim/Oblivion and fix a lot of bugs.
https://www.nexusmods.com/morrowind/mods/26348
https://www.nexusmods.com/morrowind/mods/45096/
Script Improvements can also help, though I don't know if it even touches that particular script.
https://www.nexusmods.com/morrowind/mods/43828/
And keep in mind most of these mod fixes might rely on you having an old save. Like, that script fix likely would only work at the time the disease is supposed to be removed and do nothing for you now (but it's worth a try.)
Normally it should cure your disease, but you gotta restore attributes normally (because the nature of curing it is that it's supposed to just remove the bad effects of corprus while you keep the hood effects like immortality and increased strength, so they have it that way because it keeps your upped strength and endurance forever).
May have also been a glitch due to having a spell absorption /reflection /resistance, etc etc. As fyr casts a spell on you when you drink it, it could have absorbed or resisted the actual cure (kind of like how you can resist or absorb the cure from an altar)
Also here[en.uesp.net] it's mentioned that there is a bug that if you get infected from one corprus infected NPC, then your main quest gets bugged and you have to reload a game (or maybe remove it through some console command or script?)