Update to the latest version (git pull), restarted it...
Still the same!
I have set an option "--fee 5.0", will it affect my current payout?
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Well, your payout has gone up again, but it will take a day or so of constant running to push that payout rate back up.
The fee shouldn't affect you, since the --fee tag is only applied to people mining on your node with their payout address as a username, for example if your running a public node. And even if you did do it that way, those fees should be put into the wallet on your P2Pool node.