Based on the advice from a previous thread, I downloaded Tes3cmd and cleaned the esp files in my current setup. I have MGSO 3.0 and a few other things (All LGNPC and the Less Generic Morrowind / Tribunal / Nerevarine).
I was amazed by the number of duplicate reference, junk-cell, and redundant CELL.AMBI / CELL.WHGT references found almost everywhere.
(AtmosphericSoundEffects-3.0-Tribunal.esp from MGSO 3.0 had nearly 1000 redundant CELL entries, for example).
A couple of things really surprised me. First, the MPP (Morrowind Patch 1.6.5 Beta (BTB Edit).esm) had 1 duplicate object, 39 duplicate records, and 178 redundant CELL.WHGT entries. I wouldn't have expected problems with the MPP! Am I really doing this correctly?
Second, after fixing all of the esp / esm files, I noticed that they were re-dated to the current date / time, so I ran MLOX, and was surprised to find that the load order changed. (about 20 entries were moved). In my understanding, this should not have changed the load order. Any idea why this would happen?
I have used TESP CD previously, and it had not found any issues, so I was surprised with how many things that Tes3cmd changed. I updated my saves with Wrye Mash, and after playing for a while, everything appears to be working, but still I would like confirmation that the results I am seeing are normal.
Thanks for your help!