Update
Well I have discovered that I don't have permission to open anything I download using save target as... (confusing because it now renders that function useless)
Since I could only see the invisible files when I was selecting which folder location to download to, I simply downloaded something and right clicked on one of the files with the padlock symbol on it. I clicked properties to look for differences between the files i couldn't open and ones that I could.
I found that the security tab had different permissions then the that of a file I can open. Files that I could open had a permission designated to Users (myname\users) while ones that I couldn't open we're lacking this permission. When I try to edit the permissions for...