I'll need to know exactly which version of 3.x you are using and also if you checked the location of your permissions yml files. It might be easiest if you could zip up your whole plugins\permissions directory and post that here as well as your server.log.
You will need to rar everything in your plugins\permissions directory and your server.log and post a link to it here.
Phoenix does seem wrong. Are you sure you aren't running 2.7.4 or running both 2.7.4 and 3.1.6? Post your server.log here first on pastebin.com. I just need the server startup log.
I just confirmed that Phoenix is the old 2.7.4 version so depending on which version you want to run, I have a feeling your problems are caused by the files being in the wrong location. 2.7.4 needed a file named plugins\permissions\<worldname>.yml.
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