Having this happen as well and started noticing it around the same time ago as your initial post. For now I've been manually correcting it by going to 'Downloads' and then double-clicking each mod and adding SSE as a game for that mod and then removing Skyrim: VR, but a PITA to do for each download.
I could swear I've had this happen before, long ago, and figured out a permanent solution, but it's eluding me now.