This is what I suspected, but I'm not sure why it's happening.
But now for the second experiment, which I asked you to perform earlier. Turn off all of the image variants. They're not doing anything for you anyway - they're just producing a bunch of extra files to be uploaded. Now do the same test - start with an empty output directory, make the album, wait a few minutes, and make the album again. Are you still seeing any newly-generated image files?
I suspect that the skin is remaking the folder images every time, even though it doesn't need to. It's very difficult for a skin to keep track of this, since the jAlbum core doesn't handle the production of these images (I've been pleading for a long time to have the core take over this task, since almost every skin needs these larger folder images).
But when you add all those image variants, the problem just gets worse. If the skin remakes the folder thumbnails, it ends up remaking all the variants for them, as well. I think this is why you keep ending up with large uploads after album builds that don't actually change anything.
Image variants are what I call a "solution" in search of a problem. The concept was invented almost a decade ago to address the fact that small mobile devices had poor screen resolution and severely limited bandwidth. The idea was that you could feed much smaller images to them. But that's no longer true - mobiles often have higher resolution than larger monitors, and bandwidth is rapidly approaching "free." I think they're just bloat, and I refuse to support them in any of my skins.