Be very careful about how you clean using TESTool, I'd recommend using both restricted cleaning options (Restricted Dialogue & Cell cleaning) at all times. My understanding is that the restricted cleaning modes only remove entries that are identical to stock morrowind.esm entries.
I think a lot of the problems people are reporting are due to cleaning mods without the restricted cleaning options active, this sort of over-zealous cleaning will probably break a lot of things
edit:
A few people seem to be confused about GMST entries in mods. Not all GMST entries are bad, what is bad is including the default (un-changed) values of any GMST. Loading this default value after a mod that alters the value of that game setting will undo the prior change. Remember that mods are loaded in sequential order and that anything loaded later will overwrite something loaded earlier.
Also bad are the 'evil 72' GMSTs, these are 72 tribunal/bm settings that are set to 0 and added to any mod saved w/o bloodmoon.esm or tribunal.esm active. These tend to break spells & quests from tribunal & bloodmoon, hence the bad reputation.
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