I haven't been using the weather station much for some time, just occasionally the twilight tower for breeding, before Deca took over. (I tested a few times recently since seeing your complaints.) So I could be wrong, but this doesn't sound right.
Yes, the game can set the time/weather for a particular reason. However I believe it used to be "once" ("a default" or "initial value") for the occasion. For example when the Halloween event started BFS would set the themes to Spooky + Bats, or for a particular weekend they'd set the weather to raining so players without a weather station can evolve Berry to Aubergine. But I believe if the player overwrites the "default", BFS didn't touch these settings until the next time (1) player themselves change the setting, or (2) another new "occasion" happened so BFS defaulted them again (like an event just ended so they set the theme to 'None').
But now, the game is setting the themes "every time we log in to our games" - and doesn't look like it's only on double days: I just tested it again now, on a standard day, and both building's effects still got lost when I re-enter the park.