It is interesting to know what those things mean, but I still don’t know why those packages are ignored and if there is a connection to Gnome Software or Ubuntu Software Center (and if yes, which).
I haven’t changed any of the standard sources. I’ve added one source for Owncloud (probably multiple times) , but that shouldn’t completely break the operation of the 3 software applications (I would expect). Also, I can remember that those errors came up before I installed Owncloud. So there shouldn’t be a connection there anyways.