I'm going back through and reviewing RUYN, and I can see that SOL is not picking up on my paragraphs consistently. I'm going to be doing some experiments to see what works and what doesn't. Hopefully, it'll be fixed soon.
Edit: To be clear, it's not SOL's fault, it's mine. I have a really non-optimal workflow that is wreaking havoc with carriage returns and other formatting. I'm working out a process (as suggested by a very helpful reader, thank you!) that should minimize problems in the future.