Why not "Process only updated subdirectories?"
We often advise users not to choose Process only updated subdirectories under the Advanced » General options (subdirectories = folders). In some cases, the reasons are obvious, but sometimes they aren't.
If you've updated the skin, but made changes in only one or two folders (adding images, changing captions, etc.), you can end up with some pages that are made with the older version of the skin. But all the pages are sharing the same resource files, like the CSS and JS files, and this kind of version mixing can be disastrous.
Similarly, if you've changed some skin settings, but again have made changes in only one or two folders, you will end up with a mixture of pages within the album. Some of the pages will reflect the changed settings, but others won't, which is almost never the result you're after.
But there's another situation in which this setting can produce puzzling errors. Imagine an album with three folders - two of the folders contain only JPG's, but the third also has a few PDF files in it. PDF files don't have a thumbnail image, so jAlbum uses its own PDF logo. You make the album, and everything appears fine. In the third folder, the PDF file thumbnails consist of that PDF logo. But now, without even making any changes at all, you just click Make Album again. Now, the PDF logo is mysteriously absent from the thumbnail page of the third folder! What's happening here?
Well, each time you make the album, jAlbum clears out the res subdirectory of the output, and regenerates it, and that's where that PDF logo file resides. But jAlbum copies that logo file to the output only if the album contains some PDF files. So, when you make the album again, jAlbum doesn't process the third folder (the folder hasn't been updated, and you've told jAlbum to ignore a folder that hasn't been updated). It doesn't see those PDF files, and therefore doesn't think that it needs the PDF logo file in the output. The logo file doesn't get copied to the output, and is now "missing" from the thumbnail page for the third folder.
This "missing logo" problem can easily occur in any album that contains objects that don't have thumbnail image - PDF's, zip files, Word documents, and so on.
For these reasons, the Process only updated subdirectories option is a dangerous one, unless you have a very clear understanding of how the album-building process works. The penalty for leaving it unchecked might be a bit of extra processing time, and the uploading of a few files that don't really need to be updated. But jAlbum won't generate new image files needlessly, and that's where the bulk of the processing and uploading time is.
This does not mean that you should force jAlbum to reprocess all of the images and videos by choosing Make All instead of Make Album. That's just a waste of processing and uploading time. But you should always let jAlbum process all of the subdirectories, whether they've been updated or not.