Maybe you could reproduce the problem, and paste both of the lists (the unsorted from the left and the sorted from the right) here, and we could take a look at them. There should be at least one place in the sorted list where the numbers are out of sequence.
Not necessary. The fault is on my side. What's happening is that mlox lifted two groups of mods (6-10 in each) from my list, and proposes switching them out, without any internal changes within each block. And of course, the numbers mlox references are the numbers in my list. So I was seeing
*133* Vality's Bitter Coast Addon.esp
*134* Less_Generic_Tribunal.esp
*135* LGNPC_GnaarMok_v1_10.esp
*136* LGNPC_AldVelothi_v1_20.esp
*137* Clean TC_PuzzleCanol.esp
*138* BT_Whitewolf_2_0-jms_patch.esp
*139* Fliggerty's Armor Project 2.esp
*140* Ald Redaynia Extended.esp
*141* Clean Dungeoneer Jewelry.ESP
...which is exactly what I have in my current list: same order. What I didn't notice (but should have) was that mlox proposes this:
_102_ The Hidden Pathway 2.0.esp
_103_ constance1_0.esp
*133* Vality's Bitter Coast Addon.esp
*134* Less_Generic_Tribunal.esp
*135* LGNPC_GnaarMok_v1_10.esp
*136* LGNPC_AldVelothi_v1_20.esp
*137* Clean TC_PuzzleCanol.esp
*138* BT_Whitewolf_2_0-jms_patch.esp
*139* Fliggerty's Armor Project 2.esp
*140* Ald Redaynia Extended.esp
*141* Clean Dungeoneer Jewelry.ESP
_102_ The Hidden Pathway 2.0.esp
_103_ constance1_0.esp
As you can see, placement is all.
I'm not sure why these two blocks are being suggested for swapping about, however. More confusing still, each has a couple of LGNPC mods in them. Logically, if mlox wanted to switch things around, it would tend to group the LGNPC mods. But it hasn't, so there must be other issues at work in its suggestions. Just wish I knew what they were.