It seems the combine mode action has changed as well. I've always had it in never combine mode, and until now they would still get combined when there are enough to fill up the taskbar. With this most recent update they don't, and instead go onto another row. Maybe that's related to close all windows not working. In any case, close all windows only shows up it's set to always combine. I often have 20+ pdfs open, so I want it there when they're not combined.
Never combine has always does what it says and will never combine. If the taskbar is multi row it will wrap to another row or if there is no room it will switch to scrolling.
It sounds like you want sometimes combine.
The menu option issue is resolved in 1.47 which is in beta now and hopefully will move to release shortly.