I'm ashamed it took this long to find this, but checking the "Enable Virtual Reality Headset" option in the VR settings fixed this for me. I've been using the --force_enable_VR switch so long I forgot that setting even existed. With this setting ticked, the startup argument is irrelevant and DCS is starting in VR every time.
It looks as if the last patch introduced a race condition that affects reading launch arguments but not config settings.
To avoid having to launch DCS twice now when I want it in 2D (the first time to change the setting), you can modify the ["enable"] = true value, the last line below, in [Saved Games]\Config\options.lua. It has the same effect as changing the setting in-game.
options = {
["VR"] = {
["bloom"] = false,
["box_mouse_cursor"] = true,
["custom_IPD"] = "62.4",
["custom_IPD_enable"] = false,
["enable"] = true,
Hope this helps somebody else.