Just downloaded the 1.6.3 update, after I logged in all leaves look like on fast graphics. Restarting didn't help.

I'm using these resourcepacks:

Also forge 14.23.2.2611 and Optifine 1.12.2_HD_U_D1
list of mods:

Now feedback: I didn't notice anything super weird but andesite and cobblestone textures being a bit too different from stone so they don't really blend anymore

EDIT: Optifine connected glass should really be a thing :)

Unsure. I will test, but downloading the latest 1.12-plus resource pack directly from github here results in transparent leaves.

Disabling Optfine will fix it if you're using the version from Curse. The repo has the latest leave changes that a pushed a couple days ago; those charges fixed the leaves transparency.

Can confirm that removing Optifine also results in transparent leaves. Yet the newest 1.12-plus branch here has transparent leaves with Optifine I am confused lol. The newest version of Unity for 1.12.2 on curseforge contains Antique Atlas support while the 1.12 plus branch does not. However the 1.12 plus branch contains support for Thermal Expansion/Foundation and Gravel Ores. I had thought the 1.12 plus branch was a more up to date version than the curseforge branch, but it seems they are different? I could just be stupid too.

Sorry CyanideX, I missed your statement before posting. Thank you for clarifying.

No problem.

The repo is missing a few mods and will be readded once fixed.

Regarding Andesite, I don't think it ever really matched stone. 😉 Cobble might change slightly.

Is there a way to avoid this?

also the bottom texture of daylight sensor is broken

It looks like you're missing the blockstate json. 😕

Yeah, I'm experiencing the leaf issue myself. I just found out about this texture pack and love everything but the leaves not being transparent, then I saw older pictures of the texture pack that were correct and realized its a bug. It seems to be only vanilla leaves I think.

Does this leaves bug happen without OptiFine?

Nope, just checked, all blockstate jsons are there

1. separate issues should go in separate issue tickets
2. I believe this is a bug with BetterFoliage connected grass

Definitely Better Foliage's connected grass. Had the same issue myself.