Aha, I see what the problem is now. Thanks for replying again.
I was backing up manually without shutting down, and overlooked different scenarios. While keeping the idea that the fix is to remove the leading /, a quick interim fix would be to change the add2file program. For example, if modifying the .cxx, you can change line 33 to fout << chooser.value()+1 << endl;
This brings up some problems with some scripts related to this that will be looked at.
FYI, that error in backup_status is generally a "safe-to-ignore" warning from tar and it does not mean that it modifies your .filetool.lst at all.