I was having the same issue, I did weather clear and then restarted the server and it came back sunny, and weather seems to be functioning correct now.
After much further investigation, my server has mcmyadmin running it, which in turn seems to have plugins/mods loaded in that I was unaware of. There was a sleep plugin that was turned on and that seems to have been causing the issue
I was having the same issue, I did weather clear and then restarted the server and it came back sunny, and weather seems to be functioning correct now.