I've been playing around with a few mods, and making custom icons for them, but the [item] links in the tooltips always have messed up small versions of the icons. I copied the mod.js example to my server, with the exact example icon sheet file, and it worked as expected. I literally opened the icon sheet file in photoshop and saved it as a new transparent png file, however, and I have the same result as the ones I created from scratch.
I don't see any significant differences between the two image files, both are 24-bit PNG images with transparency, so I'm missing something here.
My saved file: