I created an album in jAlbum desktop and then uploaded it to my jalbum page. After doing that I realized one photo was in the wrong sub album, so I moved that photo to the correct folder on my computer and renamed it and then renamed all the other files in both the folder the photo came from and the one it was now correctly placed into. Once all was adjusted on my folders I tried to update the sub folders in jalbum through the make album>make changes command, which didn't work. I then tried just make album and that didn't work either. I then deleted both sub folders and recreated them, and so in jalbum desktop all the corrections appear to have been made. I then tried uploading to my page but the changes did not take. I went so far as to delete the album from my page and re-upload but again it keeps showing the original structure with the one photo in the wrong sub album and none of the photo name changes are showing on the uploaded album.
Don't ever use Make Changes. That does not do what you think it does. It processes only settings changes, but doesn't process images, even if they need to be processed. Unless you fully understand that, you should steer well clear of it. Stick to only Make Album, and do not choose Process only updated subdirectories, which can lead to problems, especially with some of the newer database-driven skins.
If the local preview showed the album the way you expected it to, and the upload was successful (no errors), then if the album isn't appearing correctly when viewed from the web, that can mean only one of two things - you uploaded the album to the wrong location, and you're still looking at the old one, or you simply haven't cleared your browser cache.