If you install the trackball-not-required version of Amon_RA, it will store Nandroid backups as BCDS - Boot, Cache, Data, System. As you may guess from that, the difference is that the Nandroid backup (and restore) now handles the /cache partition, where the system Dalvik cache is stored.
You say that they will not "flash", but you don't flash backups, of course - you restore them, from the Backup/Restore menu. I'm not sure why they woud not restore, though. By any chance, did you unroot and then re-root the phone without re-installing the Scary Alien version of Amon_RA? I'm not sure what Nandroid restore does with the older version of Amon_RA if it tries to restore a BCDS backup - though, of course, any new backups will be BDS.