I've searched the forums and noticed other people are having this problem. I have found a fix, but I'm not sure if it will work with everybody or not:
1. Using the tape giving the end marker unreadable message, copy that data to a blank piece of media.
2. Erase, retire, and delete the old tape.
3. Rescan and inventory the tape and Backup Exec treats it as scratch media without the end marker unreadable error.
This helped me, hope it helps others as well.
