http://paste.md-5.net/juvasahoba.sm
I have two permission groups I want to work with separate cool downs then the default one.
I am not sure what cooldownPerPermission means.

In order for the config to actually load I had to comment out the whole permissions section.

permission:
limit1:
cooldownPerPermission: false
resetOnDeath: true
permissions:
- group.patriot
- groups.patriot
home: 0
home-named: 0
sethome: 0
sethome-named: 0
spawn: 0
spawn-named: 0
groupspawn: 0
homeinvitetp: 0

limit2:
  cooldownPerPermission: false
  resetOnDeath: true
  permissions:
    - groups.citizens
  home: 5
  home-named: 5
  sethome: 0
  sethome-named: 0
  spawn: 5
  spawn-named: 5
  groupspawn: 5
  homeinvitetp: 5

Is this a duplicate of #33? Can you confirm this is still an issue on the latest build on Jenkins (build 607)?

I believe this issue is a dup of #33, closing it. Please re-open if the fix for #33 didn't fix this for you.