This is a pretty unusual problem -- I can't remember anybody reporting it before. You might be right about affinity since the presence of HotkeyNet might change the way Windows schedules threads. I would try setting all your WoWs to run on all cores and see if that changes anything. HotkeyNet has an easy command for that:

Code:
<Hotkey F1>
   <SendLabel ...>
      <SetAffinity all>