During development of my resource pack, Immersion, I came across another texture bug, somewhat akin to the custom particles bug I posted earlier.
For some reason, the Wattle and Daub textures are not supported in higher resolutions, or at least not at a 32x32 resolution. I was not using any additional mods (I even tested without optifine or fastcraft, and experienced the same results). I tested a downscaled version of my texture, and the texture did show up, so the issue is not merely with using alternate textures. Here are some screenshots with captions to further demonstrate: