I assumed the hopper was full. If you are only putting a couple shots worth of beans in the hopper, your grind will shift as the hopper empties so there will be a grind difference between the two shots.

I got it! It was a temperature issue. I let my machine sit for 30 minutes before using it and about 5 in between the two shots. I still did a flush before each shot. But they both poured, looked, and tasted as identical as I could tell (I had the grind set for a ristretto so it'd be very easy to tell if the second poured faster). Tomorrow I'm going to see if a 20 minute warm up is enough, but 10 definitely just isn't working.

If that didn't work, I was going to try the "use the second dose for the first pour" advice, but no need for that yet. And yes. My hopper is full, so I should be getting a consistent grind.

Thanks for all the help!