As the OP I wanted to come back and close the loop on this. Short answer - I'm not a very good bike mechanic (but I try!).

When I changed stems...somewhere along the way I accidentally loosened the compression plug that sits inside the carbon steering tube. I didn't know this at the time. I didn't know what it looked like before (lesson learned - use phone for quick photo), so when the compression nut was sitting 5mm or so above the steering tube I didn't know that was wrong. So I need extra spacers to clear this additional height. Fortunately I called the bike shop, explained what I was seeing, and they set me straight (sometimes you just have to see it in person, or photos).