ZDoom

Unlikely. Mods cannot change internal CVARs. That is, unless you use Zandronum and its ill-motivated SetCVar ACS-function.

Maybe some mod made this. If the setting can't be changed in the settings, that might be it. Good thing, I don't use too many mods, so it'll be probably easy to know which one it was.

[quote]
gl_mask_sprite_threshold=0
gl_mask_threshold=0
[/quote]

No idea how those ended up 0. The default is 0.5 and setting them to 0 will indeed disable the alpha test.

Interestingly, it's fixed. I killed off my config file and started from scratch. No transparency issues now. Just to be sure, I checked with the ini files in the OP and the issue is still there.

That's not going to help, thoug because it introduces other issues because it can no longer treat alpha-masked textures as solid.
The problem here is that for some reason the alpha test in the shader does not work. I have no idea how that may even be possible.

The only thing that I've found that helps with this issue is to have the textures with transparent bits have a slightly transparent value, something with an alpha of 254 is enough to make the textures look decent again.

Have you tried changing the texture format in the OpenGL menu in-game?

Turning all driver settings to their defaults didn't help. I'll run through some more tests on GZD/QZD...

Hmm... Interesting...

Thanks for moving it! :)

I'll have a deep dive into the driver then.

I'm sorry. Unfortunately this is a driver issue - there is no bug here. :(

I've gone ahead and moved it to the appropriate forum for you, though. With the info you provided there might be someone who is able to help you with this.

Running GZDoom 3.2pre-401-g5c7b1ee8e / QZDoom 2.1pre+114+g7a1628458. Tested also in GZD 3.1 and QZD 2.0.

System is:
Manjaro 17.0.2 64Bit
Kernel Version 4.4.79
intel i7 6700
32GB RAM
NVidia GTX 1050Ti with driver Version 375.82 (OGL 4.5.0)

Happened also on earlier versions of kernel/driver/engine starting with the 2.0 branch of GZD.

Here's a shot of GZ running in OGL with doom.wad (Ultimate) at the end of E1M1:
[imgur]http://imgur.com/nNSgW9d[/imgur]

A reference shot with brutalv20b-R3 in OGL/Software mode, as it appears on blood patches too. There's quite some Z-Fighting going on, but that's irrelevant for this... :)
[imgur]http://imgur.com/VWQ3vyJ[/imgur][imgur]http://imgur.com/V3SH6VE[/imgur]

Same happens in vanilla HACX again in OGL/Software
[imgur]http://imgur.com/SewcNOt[/imgur][imgur]http://imgur.com/N1Bzvvv[/imgur]

Also in Hexen...
[imgur]http://imgur.com/nhRSRFq[/imgur][imgur]http://imgur.com/dg9EITe[/imgur]

It seems to be related to these other 2 threads:
https://forum.zdoom.org/viewtopic.php?f=7&t=57101
https://forum.zdoom.org/viewtopic.php?f=7&t=57108

My .ini files are attched in the zip file.

If there's more info I can provide, just let me know how. I more end user than coder, but I can figure stuff out... ;)