The Reset button shuts down everything except autoPause.exe. I believe that including autoPause.exe in the Reset function would address the issue.
Off-topic, I have also modified autoPause to play video only when the desktop is active. As a result, when I select a window, the playback will pause. Here is the complete code if you're interested or would like to provide it as an additional version for users:
#NoTrayIcon
While 1
$activeWindow = WinGetTitle("[ACTIVE]") ; Get the title of the active window
If $activeWindow <> "" And $activeWindow <> "Desktop" Then ; If the active window is not the desktop
; Send the pause command to mpv
Run(@ComSpec & " /c " & "echo set pause yes >\\.\pipe\mpvsocket", "", @SW_HIDE)
Else
; Send the resume command to mpv
Run(@ComSpec & " /c " & "echo set pause no >\\.\pipe\mpvsocket", "", @SW_HIDE)
EndIf
Sleep(1000) ; Check every second
WEnd