Andrew Shell dug in and found the source of a problem in building rivers.
If River4 started to re-load the OPML reading lists while a build was going on, it could cause the rivers to skip items that shouldn't be skipped. The problem would correct itself quickly on my server (made it hard to track down the problem), not so quickly on Andrew's.
The problem was pretty easy to fix, after reading Andrew's thorough description.
I had to arrange things so that the list-reading happens after the rivers are built. I put a one minute cushion in there. Have a look at everyFiveMinutes () and everyMinute () to see how it was done.
The new version is on the River4 repository.