Micha - I think the reason only the 'unsharp' are detected is because they are some of the smallest. I think the other targets may be too big for the automatic target detection to work, If you search on here for Target Detection Failure, you can find a number of threads on this subject, including this one on exactly the same subject, in which Agisoft advise that the central black circle should occupy no more that 70 pixel diameter.
http://www.agisoft.com/forum/index.php?topic=5777.msg28149#msg28149(I would also suggest that you increase the depth of field in your photographs, it looks like everything is locked to the nearest edge of your base; also try and get the frame better filled with your subject - I guess the cup only occupies 5 - 10% of the frame.)
Dave