Morrowind doesn't like when plug-ins re-shuffle .ESM dialogue order. That was a big issue I discovered with Morrowind Patching --one you more or less needs to create new dialogue in the correct order rather than sort existing dialogue. Single dialogue lines can be shuffled without incident. A group of existing dialogue? No go.
Now, if you directly edit the ESM dialogue order, then it will work, but redistributing the master files for that would be a hard sell for end users.