There's weird issue with colored item names, they get these weird symbols in front of them. It adds this A sorta symbol in the name and lore. Image attached below:
http://imgur.com/a/wCPi5

This is due to file encoding. You need to save the file as UTF-8. This can be done using more advanced editors such as Notepad++ and Sublime Text.

The thing is that the item was given by a different plugin, which has a config file edited by Notepad++. When it's given, the name and lore are fine. However after a while (usually after the server restarts a few times or the player swaps worlds) the name changes

(Dumb question but how do I reopen an issue?)

The issue at hand is still an encoding one. Not EssentialsX's fault. This is commonly caused because the file is not saved in the expected format, which is UTF-8. Set this JVM argument -Dfile.encoding=UTF-8 and see if it fixes the problem.

java -Dfile.encoding=UTF-8 -jar Server.jar

In the bottom of this comment box there should be a button that says Reopen.

I don't see the reopen button, but I'll try out the JVM argument and see if it happens again. Thank you for your help!