Some server resource packs have "blockstates" and "models" folders copied from minecraft.jar (probably for X-Ray blocking). This causes invisible blocks in this mod.

Resourcepack with all files causing the problem:
sample resource pack.zip

Enable "Force Resource Pack Compatibility" in the Block Entity Settings menu/ModMenu configuration menu for EBE, and let me know if it works

(As a side note, a server resource pack is a very poor method of x-ray prevention if you have players using client side mods like EBE, but I understand that it's none of my business to tell people how to run their servers. From my own personal experience, I would suggest block scrambling anti-x-rays, which work well against both resource pack and client mod x-ray cheats at the cost of some networking performance)

Now I noticed that the "Force Resource Pack Compatibility" option with LambdaBetterGrass makes the chests invisible even without any resource pack

Enabling the "Force Resource Pack Compatibility" option resolved the issue. However, when I use LambdaBetterGrass, this option doesn't work.

latest.log