My Windows 10 version is 1903(OS build 18362.418). I had 7+ taskbar tweaker version 5.7.1 installed and set virtual_desktop_order_fix to 1. But this virtual_desktop_order_fix seems to stop working occationally a while ago maybe after 1903 update I guess.
Reproduce steps on my computer
1) create 3 empty VD(virtual desktop)
2) switch to the 2nd VD and launch File Explorer, notepad, cmd in order
3) switch to the 3rd VD and launch File Explorer
4) switch to the 2nd VD and drag File Explorer position to the middle between notepad and cmd
5) switch to the 1st VD and then back to the 2nd VD, the order is correct, File Explorer still in the middle.
6) switch to the 3rd VD and then back to the 2nd VD, the order is wrong, File Explorer jumps to the left side.
You can switch between these 3 VDs and see the position of File Explorer jumping back and forth on the 2nd VD. If you drag the position of File Explorer to the right of cmd on the 2nd VD, then it works correctly again. The position of File Explorer always stays at the right of cmd on the 2nd VD. I also found 7+ taskbar tweaker to have this same issue with some other applications running, but this is the easiest way I could reproduce it.
Customer support service by UserEcho