Hello, I am currently starting my own Spigot 1.8 server.
The second time I started up my server, all pex commands and subcommands ingame and inside the console returned the "Unknown command. Type '/help' for a list of commands." message.
One large string of text in the console log, I think, could be the reason PEX is not working:
[08:32:57] [Server thread/ERROR]: Could not load 'plugins\PermissionsEx-1.23.3.jar' in folder 'plugins' org.bukkit.plugin.InvalidDescriptionException: Invalid plugin.yml at org.bukkit.plugin.java.JavaPluginLoader.getPluginDescription(JavaPluginLoader.java:162) ~[spigot-1.8.jar:git-Spigot-550ebace-7019900e] at org.bukkit.plugin.SimplePluginManager.loadPlugins(SimplePluginManager.java:133) [spigot-1.8.jar:git-Spigot-550ebace-7019900e] at org.bukkit.craftbukkit.v1_8_R1.CraftServer.loadPlugins(CraftServer.java:291) [spigot-1.8.jar:git-Spigot-550ebace-7019900e] at net.minecraft.server.v1_8_R1.DedicatedServer.init(DedicatedServer.java:152) [spigot-1.8.jar:git-Spigot-550ebace-7019900e] at net.minecraft.server.v1_8_R1.MinecraftServer.run(MinecraftServer.java:505) [spigot-1.8.jar:git-Spigot-550ebace-7019900e] at java.lang.Thread.run(Unknown Source) [?:1.8.0_91] Caused by: java.util.zip.ZipException: error in opening zip file at java.util.zip.ZipFile.open(Native Method) ~[?:1.8.0_91] at java.util.zip.ZipFile.<init>(Unknown Source) ~[?:1.8.0_91] at java.util.zip.ZipFile.<init>(Unknown Source) ~[?:1.8.0_91] at java.util.jar.JarFile.<init>(Unknown Source) ~[?:1.8.0_91] at java.util.jar.JarFile.<init>(Unknown Source) ~[?:1.8.0_91] at org.bukkit.plugin.java.JavaPluginLoader.getPluginDescription(JavaPluginLoader.java:150) ~[spigot-1.8.jar:git-Spigot-550ebace-7019900e] ... 5 more [08:32:57] [Server thread/INFO]: Set PluginClassLoader as parallel capable
Any help on this?

I believe this error means the PermissionsEx-1.23.3.jar file was corrupted when it was downloaded.

Try downloading it again from this official download location and let me know if you still get the same error.

Thank you, that seems to have solved the problem!
I did download the version 1.23.3 jar from the official Bukkit page, but I was unsure of downloading version 1.23.4, since the files page says that the version only supports versions 1.9 - 1.11.
Again, thanks for the support.

Excellent! You're welcome. :)

And sorry about the file version notices on the Bukkit site. Bukkit was originally very restrictive in which versions we could assign to a file, even though a file was functional in other versions.

Don't hesitate to post again if you run into other PEX issues.

Help me please, I am having the same problem, and is that every time I put the permissionsEx everything works fine and everything, but when I start the server again I get the following error and I do not know how to solve it, if they help me I would appreciate them heart.

ERROR Could not load 'plugins/PermissionsEx-1.23.3.jar' in folder 'plugins'

I already try to re-install the plugin as they say in this post but it just does not work for me, and it's very stressful, I'm new to this and I stress very fast.