If the game has a Lain WT mod, for me the game updates and the new update gets played when the mod updates. It's nothing new and I keep being surprised by the many people who don't understand that mod update and game update can't happen at the same time.
Be patient, she always comes through

And yea, removing the old mod download for the duration between game update and mod update is a nobrainer with so many reading comprehension challenged people around.
EDIT: Although, I gotta admit, it is a bit weird to not see any mod update for the end of month game updates by now. Usually works her way through them and has some posted by now.