The Edit feed source screen feed import works independently of the main feed import mechanism, which is why you will see the 5 latest feeds showing up correctly, but then not showing up in the main aggregator.
Whenever you edit a feed source the aggregator will recheck all feeds, which explains why doing the minor edit trick will refresh things and they will show up correctly. The issue seems to manifest itself therefore when the aggregator is doing its own hourly update via cron.
In the meantime I have set up a test site with some of the troublesome feeds that you've mentioned, lets keep an eye on feeds in the coming days, as soon as you notice a duplicate or missing feed let me know so I will see if this happens also on mine.
Here's a screenshot of my feeds at the moment, everything works fine, but I'm monitoring them going forward.