I have recently ran into this issue on my laptop, after loading up a shader. Setting the shader off didn't fix the issue. I have tried to tweak the graphic settings and it looks like the glitch only occurs when the Trees are set to either Default or Fast.
After some digging done on the Optifine issues, I found out that is the way this should work - the lowest quality set for the trees sets the leaves to opaque, while the 2 better quality settings have the leaves on transparent.

Taking into consideration the fact that the glitch is caused by the way Optifine is supposed to work (I guess), I will leave this here in case you weren't aware of it.

On a side note, do you intend to update the textures/objects introduced by the last couple of patches or is the work on this resource pack mostly abandoned?

Thank you!