I have only been using WR for a couple of days now, but my copy is doing some freaky things. I launch WR in the morning, work with it all day and close it in the evening. Every once and a while when I am surfing the web or launching/closing other applications WR takes focus. Occasionally it will also tell me that it can not find one of the objects in the script, although I have not attempted to run a script recently.
Check your hotkey actions (F1....f12). It could be that you are accidentally invoking WinRunner. I have observed this in environments where WinRunner was just left on and users began using apps with hotkeys that matched those of WinRunner.
l know that you indicate that you are not replaying/running a script, but l'm sure everyone has had the instance where a script is still running without your knowledge - this would account for it appearing to run again and giving you errors. l don't discount the function key post, but l'd also check and ensure the script is actually 'stopped' and not just 'stuck'. good luck, b.