darkfader, what exactly do you mean by "automatic scanner"?
You mean a scheduled scan, or a manually started scan which has an automated action set for infected files (what action exactly is that?), or something else maybe?
Additionally, can you somehow distinguish the files that were not repaired? (you said only some of them weren't repaired... is there anything special about them? filename, size, ...?)
I cannot reproduce the problem, i.e. it probably isn't what I thought originally...