Hey guys. Now I have never heard of this problem before, nor do I believe it has been reported. It seems that somehow (maybe from BCSounds official download somehow) there are now hundreds of red floating objects in Morrowind, as well as "wtf no mesh" symbols replacing all lights and torches.
Any ideas? 
post some screen please.
Yes, those are the sound activators, they should not appear ingame only in the CS... that's strange, but also theres one glitch like that in Raven Rock, under a table you can see the same that red diamond thing. I repeat that's a sound activator, why you can see it? (ingame) I have no idea, but you can reinstall everything again without BCSounds and see if that works.
Seeya ;D
Yep I am getting rid of BCSounds. Knew that bastard was the culprit.... 
Getting rid of BCSounds seems to have had no effect. The sound activators are still present. 
There also seems to be some missing meshes for some reason or another. Torches and lamps, specifically.
Reinstall everything, but don't forget to delete the OLD Morrowind_ob.esm, Tribunal_ob.esm and Bloodmoon_ob.esm file. Delete those .esm's and run the ESP Converter.
Seeya!
PD: Have you been playing all this time (2 months) with those red floating things around?