Hi everyone, I think I resolved it. There was a component of my preamble that I've been using based on someone else's template, and it included a command that put periods after section numbers.
Just to clarify RE the minimum working example: what I had put in my earlier email was something that could literally be copy/pasted into a lyx file, so I just assumed that would suffice. I can send an actual lyx file in the future even if it is just three lines of lyx commands though!
