I did a little quick hacking of the main script of the skin, and of the user interface, that I think will do what you want. I've changed the checkbox so that it now reads, Show filename (without extension) if no jAlbum title.
If you choose that option, it will show the title if there is one, and if there isn't, the filename, minus its extension. If you don't choose that option, it will show the title if there is one, otherwise nothing (or just the comment, if you've entered one).
I made a similar fix to the thumbstrip so that, when you hover on a thumbnail, you get just the filename without its extension. I didn't plunge any further into it - the thumbstrip tooltip won't show the title, no matter what. That exercise is left to the student.
Hmmm.... No problem in my quick tests. Make sure you're refreshing the browser cache.
I'm seeing other problems in the skin, however (not the result of my changes). If there are spaces in file names, for example, they're being encoded as %20, which is technically correct, but not very friendly for display purposes.
This is the problem with orphan skins like this one. The developer was an intern who's no longer around. Anyone else wading into the skin to make changes starts uncovering all manner of glitches that need to be addressed, but the code is unfamiliar.
Attached is another beta, which addresses this filename encoding.