I do believe there currently is a bug in the latest version of spigot (Version in attachment). Here is what happens. when enchanting at lvl30 it will only have one enchantment; every single time. If I am correct you can have up to 3 enchantments on an item. When I changed to a later spigot version (1.10.2) the issue went away. And just to verify, I put the latest (1.11) back in and tried and the issue was back.

I hope to have this resolved quickly. If you need to contact me to see the issue for yourself don't be afraid to send me a message. I will respond within 24 hours.

Respectfully,
SirHigginz