CivStats had a running clock again, so I presume(d) the uploader must have been active/activated somehow...
That's cool. When the net came crashing down around me, I saved and closed the pitboss windows themselves, but I stupidly didn't take down the uploaders. So, when the net came back up while I was at work, the uploaders resumed, but there wasn't active games for them to work with, hense the errors you saw.
So I completely see where you were coming from.