What is happening is that my code has been checking for segwit transactions to not be included in old shares for months but I haven't included a check in the mining code since I thought that v17 shares would activate before segwit activates. Bitcoind is sending segwit txs in its block template but p2pool can't mine them yet. This has nothing to do with syncing other shares.

https://github.com/veqtrus/p2pool/releases/tag/17.1 if anyone needs windows binaries.