Whenever I add a new plugin, I usually do /rl (short for reload). Same thing happens for the rest of the commands said in the title. Every time after I do one of the commands in the title, the same thing happens. What I do is I now drag and drop the file into the plugins folder. Then another reload, it'll show up. It's starting to annoy me as well as the players.

Which version of Minecraft and PEX are you using?

Minecraft - 1.8.8
Pex - Tried all 1.8 versions, still does it

Show me your console log.

I've figured it out.

1. I changed from pex minecraft version to 1.11, and 1.8 was disappearing because of the other chat plugins I use. Such as TagsGUI, ItemHover, DeatMessages.

Someone help me when I close and I open the server Pex some stops working Somebody help me

Don't hijack other people's threads. You already have your own ticket posted.