I added a folder containing skin files via FTP as I usually do. I did this several weeks ago. I set the skin in the admin settings for the site and it is working. But if I try to go back in via FTP to modify the files they don't show up. I've used Filezilla, WS_FTP and CuteFTP, all with the same problem. If I add the file via the Powerdnn control panel file manger in my hosting account they don't show up in FTP programs. I'm thinking it's some permissions issue somewhere but I don't want to mess anything up toying around. Anyone experience dthis before? Any advice?

Does this happen to any other files you upload via FTP? I'm pretty sure powerdnn uses Plesk control panel, your FTP account may be incorrectly rooted. In other words there may be two copies of your files, one what plesk and IIS has access to and the other is where your ftp account is rooted. This usually occurs if hosting account has been moved to a different server, but someone forgot to move your FTP services.