I just started game like this:

Remastered Lighting v1.1 and Link To Remastered v1.1 HD Textures
ENHANCED_STORMTEXTURE_RETEX
Brother-in-Arms
Addons Pack - Adventure(alt)
TL1CP v178
Variant
Essentials - Vanilla UI
Torchlight II Essentials
SynergiesMOD
Unearthed Arcana

…and everting was fine. (¬‿¬) Even bugs that I had with basic Brother-in-Arms are gone.

So for (ﾉ◕ヮ◕)ﾉ*:･ﾟ✧LULZ I did that:

Remastered Lighting v1.1
ENHANCED_STORMTEXTURE_RETEX
Addons Pack - Adventure(alt)
General Passives For All
TL1CP v178
Variant
Essentials - Vanilla UI
Torchlight II Essentials
SynergiesMOD
Unearthed Arcana

ರ_ರ and it worked without bugs - you mentioned...

┐(‘～`；)┌ I don’t know…
game files integrity?
fragmented hdd?
bad sectors on hdd?
Anything sadly (╯︵╰,)

Thank ytou for taking the time to trouble shoot this inquiry. No failure on your part. It is just the way mods sometimes interact with another. Wish there was a magic mod that you could place int there that would see on the discrepancies and go wham! your fixed :)

Any thoughts to whay the pets no longer have the rings and necklace option boxes? Or why the shared stash no longer has the adv buttons showing at the top? does this happen with you mod load order?

I looked at “General Passives For All” workshop page and “Bug Reports” tab. It seems that someone mentioned similar problem, but claiming that Essentials is bugging with GPA.
As of my load order is mostly there
You could try latest version (35) of GPA from Nexus [nexusmods.com]
…so basically I failed you, sorry. Maybe someday I would try to put GPA files directly into this pack, or something – if I get source files.

Just to add, I have used LAO 2.0 CE, BiA Warbounds, Dracos UI Merger and Master Mod wing TL2E, SynMod and GPA (v29) And they do work fine together with none of the afforemention issues in both of these mod versions.
Thank you for your endeavour on this again greatly appreciated. One of the other Mods just doesn't like GPA it would seem also. Even without GPA still get isssue of The pet still does not get the slots for rings and necklases. AS well as the shared stash forward n back buttons not showing.

Any suggestions would be helpful if you have anything else theat might be happening. Have a good one :)

I have tried this mod with only SynergiesMod and TL2 Essentials. Still have most of the same issues from the other mod https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=1131372029&tscn=1507725390 Except for the issue with players gear. It does allow for placement in right spots (instead of anywhere). And it will give the physicall and elemental bonuses. But as soon as I add in General Passives for All (v29) I have 2 issues that happen
.1) if I place GPA at top, then this mod, then TL2 E , SynMod; i can get the tab to show on skill hud. But then i get the issue with gear not no auto place and being able to place them anywhere. And not getting the stat bonuses fr gear.
2) Load order of this mod, GPA,TL2E,SynMod; I nolnger can see the GPA tab in skill hud and still have issue with gear. as mentioned before.
Just thought I wwould pass this info along,