First, don't use
Make Changes. It doesn't do what you think it does. Please trust me on this, and just click
Make Album every time. (And don't choose
Make All, which forces jAlbum to regenerate all the images - that
will produce a massive upload every time!)
The smart upload really shouldn't be uploading everything each time. At worst, it might have to traverse the directory structure, comparing file dates and sizes, but even then, it should take no more than a few minutes.
There might be a damaged manifest file on your server. Choose
Tools, Upload/Manage, connect to your server, navigate to the directory that contains your album, and delete the
manifest.jmf that's there. If you don't see it, click the
Advanced mode icon, which will show you all the files in the directories.
Then try your upload again.