Hello Jason,
I don't know the answer to your question, but I'm curious where you got the AMEX and BATS data?
Per https://www.quantopian.com/faq#data:
We currently provide minute-level bar data of all US stocks from January 2002 through the previous trading day for backtesting...
For paper trading and real-money trading, we get a realtime feed of trades from Nanex's NxCore product. Those trades are bundled into one-minute bars and fed to the trading algorithms. Paper trading data is provided on a 15-minute delay. Real-money trading is processed without delay.
Also, are you using the Quantopian historical database (for backtesting) or the Nanex feed for your comparison? To my knowledge, Quantopian has never revealed their source for the historical data, so it is not clear that the backtest data will match (exactly) the Nanex-derived bar data.
You might consider if 0.1% is "in the noise" in the context of Quantopian's system, which, if I understand correctly, attempts to minimize latency, but does not guarantee that your order will be received at IB within a fixed sub-minute time frame (relative to the time at which the algorithm processes the Nanex-derived bar data, which has its own latency).
Grant