Been an issue for a long time now.

Basically Minecraft incorrectly saves custom item names and custom item lore.
I believe this is due to conflicting ways of saving "default" text.
Minecraft's default text is unitalicized and light grey. However, custom items are given italicized names, and custom lore is italicized/colored purple when they are created.

When the world reloads, this causes a conflict where the NBT data is written at least two different ways.

You can replicate this issue in Singleplayer by creating a loot table that generates a custom-colored item, and reopening the world. Then use the /give command to give yourself the same custom colored item. The items will not stack.
You can replicate this issue in Vanilla Multiplayer by /summoning a villager that BUYS custom-colored items. You may then use loot tables, /give or another trade to give you that custom item. When you restart the server, the trade will no longer work, and the items will not stack.

Attached is an example of how the data is changed for a diamond sword before and after a vanilla server is restarted. As you can see, the data's syntax is slightly changed.