|It is not a good thing when your directory tree shows desktop for folders and files that are not.|
This is something I would put serious investigation into. Not a virus or malware type of behavior, but definitely a registry glitch.
I would first try CCleaner and do a registry cleanup. If that fails in clearing up the problem, then I would be checking the registry in the areas where the affected folders reside.
If you are not familiar with the registry, leave the job to someone who does to have a look when they have the chance.