i'd like to address this problem as well.
at first it doesn't seem like serious issue, until i was using some options which included 'tick/untick' action in VNR preference.
i can access preference, but i CAN'T tick/untick anything inside because it kept losing focus over this ghost nvidia overlay which VNR thought it's a 'game'.
if you try deleting the game shortcut, or even delete the running 'nvidia geforce overlay' from task manager process tab, VNR will just find any nvidia program next in line to be treated as 'game'.
this is even worse when i tried to open my old VNR, and guess what, it's also affected and it acts like the new VNR i describe above.
how do i solve this issue ?
i've found temporary solution for this issue, by unchecking 'Nvidia GeForce Experience' program from running as PC startup items through 'msconfig'.
after restarting my PC, my VNR doesnt auto-grab that ghost nvidia overlay anymore.