I have just put this plugin on the server and tested with another player and seems to be fine for them but when I attempt to use the /p command it says 'You've not got enough pipes to build that I'm afraid.' which means I have reached my pipe limit but haven't even used it yet. If I give myself the admin permissions for the plugin then I can use it no problem. Do you know what would be causing me this issue? 

I have deleted the .json in the data and checked the config and reloaded the plugin. Is there a location that this data is saved so that the plugin knows how many each player has used? Ill keep looking as it would seem that would be stored on the server somewhere to be able to keep the limits in check.

You need to be granted a user level. 

Joe90

You need to be granted a user level. 

Ok so I have the user perm. Its inherited from the other parent groups. I also went through all the groups individually and enabled the perm for each group. Still doesn't work, so I did more tinkering and found out how to make it work but don't think this is how it is intended. All my groups have user and all but the hqm level enabled. All are inheriting and when I look at my permissions it shows that they are all inherited. If I enable the permissions directly on my user for all the levels but hqm it works. 

So all group permissions are set correctly and other plugins have no issues with the groups or parenting so not a group/oxide issue. I can disable the user permission on my username and it works with the levels enabled. So something in the levels are not working for some reason for me even though it shows they are inherited from the group im in which is owner but the user permission is working inherited from the group.

I may need to get some more details from you on your setup.
I've not come accross this issue before.

Last night I left the perms so that it would work for me and went ahead and built a sorting system and a few other things and today I just got on and all my pipes are gone. Only thing that I can think of is that it is lost on a restart which happens in the middle of every night. Not sure what to do about that.

The pipes should save with the server and on Unload. Not sure why they would have vanished. Did it generate any error logs and what syncPipes data files do you have? 
Also just checking you have the latest 0.9.27 version as there was a fault with 0.9.26. 

I just upgraded to 0.9.27, now im getting the following error.

Failed to call hook 'OnItemRemovedFromContainer' on plugin 'SyncPipes v0.9.27' (NullReferenceException: )
  at (wrapper managed-to-native) UnityEngine.Component.GetComponentFastPath(UnityEngine.Component,System.Type,intptr)
  at UnityEngine.Component.GetComponent[T] () [0x00021] in <ba657ba1ce6746c39d9263534c2395e1>:0

  at Oxide.Plugins.SyncPipes.OnItemRemovedFromContainer (ItemContainer container, Item item) [0x00013] in <3319836cee0f4186940dbb73fbdc5d3d>:0

  at Oxide.Plugins.SyncPipes.DirectCallHook (System.String name, System.Object& ret, System.Object[] args) [0x00a71] in <3319836cee0f4186940dbb73fbdc5d3d>:0

  at Oxide.Plugins.CSharpPlugin.InvokeMethod (Oxide.Core.Plugins.HookMethod method, System.Object[] args) [0x00079] in <60c318df79ed41688ea59335e48d61ad>:0

  at Oxide.Core.Plugins.CSPlugin.OnCallHook (System.String name, System.Object[] args) [0x000d8] in <dfcb48ea05694263bbc08e62a39c274c>:0

  at Oxide.Core.Plugins.Plugin.CallHook (System.String hook, System.Object[] args) [0x00060] in <dfcb48ea05694263bbc08e62a39c274c>:0