If a user chooses "..." as the image bounds, but doesn't enter any values, then hits OK, there's a console error dump, and Make Album won't work. If the user then chooses another skin, he gets a popup error dump. This should be handled more gracefully, perhaps by returning to the previously-selected bounds when no values are entered.
Audio file or PDF with related THM, plus Link to originals, does not produce a slide image (OK for similar video situation). Causes a broken album in Tiger, for example. (My skins detect the problem configuration and do the file copying themselves.)
Bugs that produce errors or unexpected results, but that aren't often encountered:
Changing the default file naming from index and .html doesn't clear out the older files - you end up with, for example, both index.html and index.php. Uploading both index.html and index.php could produce some very puzzling results, depending upon server configuration.
File selector for webLocation representing images doesn't remember location.
After deletion of a user-installed skin, and notification that the bundled version is still present, the skin doesn't reload. The settings tabs from the deleted version remain.
Changing skin or jAlbum settings that should trigger a change in the theme image crop mask don't trigger the change until the user closes the settings panel or clicks Make Album. That means that the theme image crop focus panel isn't always getting updated when it should be.