Seems to be working OK now - ian666 in another forum said EDSM was being slow to respond - now it looks OK.
I've noticed numerous times where EDSM will have body data but it won't show up in EDD and I always have the button toggled on. If that's because of slow response from EDSM maybe the timeout should be changed or EDD should retry.
Last night I also encountered a weird desync. I think it was Cyoidai WY-S d3-0 where EDD and EDSM were showing different info--EDD had the star and planet 1, and EDSM had the star and one of the other bodies. I went ahead and did a full system scan because of that. (well, maybe I skipped some moons..)