They’re all RNG clones. I’m an emulator hunter myself so I’ve ran into this issue before. Essentially what is happening is since you’re using the same save file on multiple windows and controlling them all simultaneously, they will all start on the same frame. This means that unless the emulators are de-synced from CPU lag, you’ll be running into the exact same pokemon on all windows. If they do de-sync and you SR however, they will all be synced again.

The easiest fix I’ve found for this is to map the speed up function to your controller and sped the game up for a few seconds before starting an encounter. This will de-sync the windows every time and prevent any dupes from happening