I think this is very unlikely. You probably are an admin user.
If you are a root level user, that means that you have completely turned off the permissions on your system. That is possible, but Apple discourages doing this except perhaps for a short, specific task.
If you duplicate a folder in the Finder, that will not only duplicate the contents of the file, but also any metadata, including permissions and extended attributes.
When you do a Save As, Panorama creates a new file. So the contents of the file are duplicated, but not the metadata.
I think you have some sort of problem with the metadata for the files that are causing you problems. Perhaps a permissions problem. You might be able to clear this up with Get Info or with Terminal.app.
The puzzle is that you don't see an error message when you try to open the file. Perhaps the problem is one that trips up the old Carbon API's that Panorama 6 uses, but that Carbon doesn't report as an error properly.
It's also possible that there is a metadata problem with the folder. I've never seen the problem you describe, but I have run into problems with other programs where files could not be accessed because of permission issues on the enclosing folder.
No, nothing to worry about. Clearly the content of the files are fine. Using Save As to a new folder is an excellent approach to leaving behind metadata problems in existing files.