When do P2Pool Node Fees get paid? I have set up a node and been running for a few days now and a couple of payments have gone out form it which is good. 

These payments are going to a coinbase wallet and there is a local wallet configured for fees and the fee is set to 5%.

I have had 2 payment come out of the system at around 0.002 BTC but no fee payments have been sent to the p2pool wallet. 

Are they held to reach a certain amount or are they computed in a different way that on the payout amount. 

Thanks.
Correct - you will be awarded node_fee percentage of the shares found on your p2pool.

Relevant lines of code: https://github.com/jramos/p2pool/blob/master/p2pool/work.py#L197:L203