My config:

{
  "Settings": {
    "Enable OnNpcTarget hook": true,
    "OnNpcTarget return code (debug warning issue with TruePVE)": true,
    "Permission name": "sleeperanimalprotection.active",
    "Required to sleep ON foundation": false,
    "Use permissions": true
  }
}​

Yes, there is flag in TruePVEto prevent animal from attacking sleepers.
"flags": "AnimalsIgnoreSleepers, ...... ",

also, in the config of this plugin, make sure the "Use permissions": true
when set to false, permissions are ignored

I don't have that flag in TruePVE. I set permissions to true, as seen above. 

I just retested with that config ( Flag not set in TruePVE, and your config from the first message )
and the animals will not attack sleeper only when the permission is set.

Try to unload the plugin to see if an other plugin is protecting sleepers.