I am trying to save my collection of JS Bach's cantatas, about 70 CDs, and although I can see all tracks of each CD on the local files and playlist, when I try to save them to HD there are always some of them missing. And after trying again more are missing, until I cannot save any file at all. Then I have to restart the computer and again the same file would not show up on the saved ones. It does not with other applications(eg Banshee), and it changes when I login as Ubuntu or KDE (or any other version). But I cannot ever record the full CD, and I have tried with different labels, all possible combinations of track naming, etc. I am running Ubuntu 12.04 64, Amarok 2.5.

By "Save from CD" you mean you are ripping your CD with Amarok, right? There have been a few glitches with the audiocd KIO slave Amarok uses in the past, which exact KDE version are you using?