Here's a repro I found - if anyone can try this, please let me know if it also works for you:
This appears to happen only once after explorer has first started. I can reliably repro this by restarting explorer from task manager (explorer -> end task, then "Run new task" -> "explorer.exe"), opening a new explorer window and moving it to the background, and then using ctrl+c to copy text in any application. That forces the previously opened explorer window to be brought to the foreground with focus.