The main icon in the top-left corner is not showing up.

The option "Display main icon" is checked (as it is by default) in the Per player mod settings.
Turning it off does not work either - When I turn the option off and go back in the menu it's turned back on.

I will try to attach my modlist, but I wouldn't know which one would be interfering.

Can't upload files, but here's a prettified version from the JSON:
- base
- elevated-rails
- alien-biomes
- alien-biomes-graphics
- angelspetrochemgraphics
- angelsrefininggraphics
- angelssmeltinggraphics
- auto_manual_mode
- better-victory-screen
- bobinserters
- boblibrary
- boblogistics
- boxing-button
- CleanFloor
- configurable-valves
- CursorEnhancements
- even-distribution
- ExtraZoom
- flib
- force-inventory-insert
- helmod
- LargerLamps-2_0
- Milestones
- ModuleInserterEx
- no-remote-view-border
- nullius
- pump
- pushbutton
- RateCalculator
- RecipeBook
- reskins-angels
- reskins-bobs
- reskins-compatibility
- reskins-library
- textplates
- Todo-List
- UPSFriendlyNixieTubeDisplay

hello
It's probably because another mod is modifying the menu; try disabling QOL mods.

Other mods have no trouble showing up though:
https://imgur.com/huEIJzv

For me to take a look, it would be easier to have your save file; it's too time-consuming starting from a list of mods.
Have you tried disabling/re-enabling Helmod to troubleshoot?

https://limewire.com/d/1RAL7#zCubjlMgQV

Hope this works. Don't usually share files publically so I got one of the first Google hits..
Restarted the game to keep the file small.

I test and that work fine, the icon appear when I check the option in Per player mod settings
Are you sure you confirm change with the bottom button ?
But the mod settings menu is a Factorio menu i can't do nothing if dont work

Another way: use short button "Planner" in the tool bar or short key