Permissions EX permissions not working

Hi everyone I use the Permissions EX plugin for my Craftbukkit server. Its permissions do not work and I would appreciate the help to understand why. Thank you! I keep having "schema-version: 1" pop up and messes up my whole permissions file. What is this?
groups:
default:
permissions:
- modifyworld.*
- spleef.join.1
- essentials.warp
- essentials.warps.*
schema-version: 1