In Windows 10 there is a new feature to allow scrolling of inactive windows when hovering over them. For instance, if the active window is from Chrome and there is an inactive window from Thunderbird partially visible, I can scroll the Thunderbird window without switching to it first. This feature does not work when a Claws window is the active window (it didn't work with Claws 3.12 either).
This may be an issue common with GTK+ applications on Windows in general. Alas, I do not have access to any Win10 machine, so I don't think I will be able to do anything about it anytime soon.