I think that the help file is stating that if you are scheduled to d/l from the weather-station at 12:01, 13:01, 14:01, etc., and WL has been started (or restarted) at an odd time, it will sneak in a download to catch up. The help file also states that the auto-download schedule is in addition to (optional) download requests by internet upload profiles. It the problam that it just does not get back on the configured schedule and you end up with (minutes) old data in your internet uploads or an inconsistent time-stamp in your raw data files?
If that is what is "mucking up" your system scheduler, are you trying to run windows command macros to d/l instead of the method above? That doesn't seem necessary, so I must not completely understand your situation.
[edit] I just noticed you have WL-IP, so that may not work quite the same as my WL-USB. Sorry if I confused things further. [/edit]