No, I built a p2pool for myself so I'm the only miner and mining an altcoin.
Everything works fine except the incoherence.
The transaction number and payout times showed from my wallet always far bigger than P2Pool outputs.
Eg. P2Pool shows there are 43 shares in chain, but I already got paid nearly 60 times and I can also see 60 blocks and transactions in my wallet.
The share chain in p2pool is the PPLNS payment database, in effect. It does it that way so that a network of nodes can work in a trustless way, like how bitcoin/etc function with proof of work adding blocks to the blockchain.
So with 43 shares found so far, since you are just mining by yourself, your entire PPLNS payment database has 43 entries. For each miner (just you), you add those up and that is the amount you are due when a block is found (proportional to other miners also in the sharechain). You can see the amount of payout you'll get if a block is found on the default interface by clicking Payouts. Since you are the only miner, if all of your mining goes to just 1 address, then the Payouts should match the block reward (plus transaction fees) and all going to your address, I believe.
So that's just to determine how much you get paid. When you get paid depends on when you find blocks. For every block found, the pool pays out to everyone on the share chain based on the above. Finding shares on the share chain doesn't pay you, it just sets how much you'll get paid when a block is found.
If you've been paid 60 times, then you've found 60 blocks while having at least 1 share on the share chain.
Hope that helps?