I suggest you run Norton Disk Doctor. I had a major system crash after my iMac starting behaving the way you describe. I would open a folder on the desktop, it would appear empty, I would close it and open it again, and the files would be there. Later, I would try to open it again and it would be empty again. NDD found a lot of problems with the catalog file. I still don't know what caused it, but NDD fixed it.