Command block not detecting items. Please help!

I run a Paper Minecraft server and I use shopkeeper and custom crafting to for custom items with special abilities. I have command blocks that detect when a certain named item is in my inventory and it does a thing but whenever I put one of those items in custom crafting GUI it doesn't work unless i rename it in an anvil. Also if I restart the server I have to rename the all items in an anvil again. Also I had a different server in 1.14 that ran the same plugins but was completely compatible with my command blocks.