I believe I have the same issue, which is related to the way OBS studio is attempting to find applications to hook on to.
I write my own OpenGL based software with the GLFW library, and unfortunately, this library uses the same Window class name for every instance of the application I spawn, thus every Window that GLFW creates for me has the class name of "GLFW30". As a result, OBS is not obeying my choice to detect the game capture or window capture source by title name.
When setting up the game captures, I can initially get it to differentiate between the separate OpenGL windows which are all from different processes, but as soon as one changes scenes to a scene that doesn't use one or more of the captures that I have setup to detect by title, and then switch back to the original scene. All the sources hook onto the same window of the same process. The processes spawned that make use of the GLFW library are from the same physical executable on disk as well which may be a factor in OBS getting confused over what to hook on to!
TLDR: Game or window captures with the same executable and Window class name which are from different pid's are bugged when changing scenes because the choice of detecting the application window 'by title' is not being obeyed.
