I stopped using the automatic eject for a number of reason, but had similar issues to what you are experiencing as well.
What I found was that delaying ejects and reports until I was ready to do the ejects for offsite, that i better used media, since they were still in the robot, it filled the tape. Also doing the eject manually noted that the CAP was full and when I removed the tapes, if it did not find it automatically, then I would just hit the key to continue. Since reports are dependant on the media being ejected from the library, delaying reports until the ejects are done made sure the documents are in sync as well.