I have only been using storeBackup for 3 weeks, so I have always run the latest version. The files are many different types, but they seem to be larger files - mp3, wav, tiff, jpg, iso, etc. Only scattered files of these types have problems, not all of them (250 or so out of hundreds of thousands). No text files appear with incorrect checksums.

One thought: these appear to be the same types that storeBackup is not supposed to compress. My config file says

addExceptSuffix= '\.JPG' '\.GIF' '\.PNG' '\.jp2' '\.JP2' '\.dng'
        '\.flac' '\.mpc' '\.wma' '\.WMA'
        '\.avi' '\.AVI' '\.DIVX' '\.divx' '\.XDIV' '\.xdiv' '\.wmv' '\.WMV'
        '\.mov' '\.MOV' '\.dvr-ms' '\.tp' '\.mp4' '\.MP4'
        '\.tib' '\.gho' '\.GHO' '\.GHS' '\.iso' '\.ISO'

I can understand that there might be a problem if the file changes while being backed up, but these are file that haven't changed, sometimes for years. My big concern is that when I delete a backup, backups that previously checked out ok now have errors, so I have no idea if any of my backups are valid or not.

Perhaps unrelated, I also get some of the following error messages when I run the backup check

Use of uninitialized value $rel in hash element at /usr/local/bin/storeBackupCheckBackup.pl line 846.
Use of uninitialized value in numeric eq (==) at /usr/local/bin/storeBackupCheckBackup.pl line 846.

I get 16 of these message pairs, which is much smaller than the number of files with mismatching md5 checksums. These came at the end of the run, just preceding the last info lines.

I am not sure how to deal md5 sum mismatches that storeBackupCheckBackup finds. I have tried just deleting the backups for the days with the mismatch, but that just seems to propagate the problem to the next backup, and makes me distrust the entire system. Specifically, I had a series of daily backups, and the first two registered errors in the backup check, but nothing in the others. I deleted those two backup directories, ran the backup again, and then third day suddenly showed up as having md5 sum mismatches. I deleted that, and then the 4th day, which had been fine, now had problems, and so on.

Did just doing rm -rf on that day's subdirectory break other parts of the backup? The docs say it is ok if not using latelinks. I have used latelinks, but also made sure that storeBackupUpdateBackup ran before I did the removal.