This doesn't seem to be the case. The file is hosted on FMS 12 Advanced and is new/under development in FileMaker 12. I Closed and downloaded a copy, then ran both a consistency check and a recover on the copy. Both passed, with no problems reported. I created a second/manual backup script on the server that verified and cloned the file. Ran this with out errors.
The main backup runs hourly and only reported the errors once. I'm considering deleting all of the backups from this script or just creating a new script. I have seen where a glitch can mess up a whole set of backups with the new linked file system the FMS uses.
Thanks for the suggestion