I would like to manually update an existing -multiple folders- album...
which files do I need to upload if I only added a new folder (with images) to an existing album?
Is it "new folder" + "index.html" file enough?
You need to upload all new and changed files. That will include the new folder, but it may also include new files at the top level, changed files in the sibling folders, and new resource files (the "res" directory). Depending upon the skin, it may include new JSON files.
In short, it's not easy to tell which files need to be uploaded. That's why the jAlbum upload routine is "smart" - it figures out which files need to be uploaded. You don't need to pick and choose files.
If you're using an FTP client program like FileZilla, you can tell it to upload only new or changed files, then just mark the entire output, and tell it to upload. It will hop, skip, and jump over the unchanged files.
So, no matter how you do the uploading, it's easier and safer to let the software do the work for you.
Finally, if you have updated the skin you're using, you must make the entire album using the new version (not just the new folder), and again let the software figure out which files to upload.
Those symptoms suggest only one thing to me, and that's a damaged manifest file. When you're using something like FileZilla, it's not using the manifest file - only the jAlbum uploader uses it. It speeds things up a bit, but can also cause problems.
Connect to your hosting server, navigate to the directory that contains the album, and delete manifest.jmf. Then try the jAlbum uploader again.
(For my own stuff, I often stick to FileZilla. Go to File, Edit, Settings, Transfer, File exists action, Uploads, and choose Overwrite if source file newer. Then, you can just mark the entire contents of the output directory and tell FileZilla to upload it. It will blow past the unchanged stuff pretty quickly.)