I have had odd quirks before with absent rooms, I think in my case (it was quite a while ago) I chose to export perhaps a dozen or two rooms, and some of them appeared. It might be worth letting John Elliot know about this in case he one day plans any updates. AFAIK the last update was 2015 (or 2012, not sure) , he does have an account here but I'm not sure if you decided to contact him if a PM here or an email via his site would be best.
You can sorta fix this by putting a newline before every <room> tag in the xml file JSWED generates. That makes JSWED read all the rooms, however guardians, conveyors and other stuff can still be messed up or missing altogether.