Hmm, this sounds peculiar. I have left my 770 to download en masse countless times, and I have never experienced an issue like that. I wonder if the blanking works differently on the n800 (OS 2007) as it does on the 770 (OS 2006). It's possible that OS 2007 is sending applications different signals based on blanking events, which may disrupt Maemo Mapper's interpretation of the signals.
That long label is not long enough to describe the actual functionality of that checkbox. Screen blanking is only prevented when your current position changes, which means you'll need a GPS device. The assumption is that you don't really need to keep the screen on if you're not actually moving. Of course, in your case, that's exactly what you want, but only because the blanking is disrupting your downloads.
Does the problem only occur in winmapper, not Maemo Mapper? I don't know how winmapper works, but it's possible that you're getting the captcha due to the mass downloading. I've never seen the captcha myself, but it has been reported by some, and that might cause 0-byte file entries, and since it's not entirely consistent, it could (for example) work in Maemo Mapper and not work in winmapper.