This is not caused by a Mod. It is a bug in Vanilla Minecraft and should be fixed there. You could argue it is irrelevant since you have no use for bigger texturepacks in Vanilla Minecraft and consider this issue resolved.
OR acknowledge that this is a shortcomming of Vanilla Minecraft and keep this open to at least get a chance that somebody at Mojang has a look at it.
In my opinion it will have to be fixed anyway if the API becomes a reality, so why not now?
The Issue occurs with a clean vanilla server and YES it is a HD Texture Pack. Just try Sphax PureBDcraft 128x128. If you conclude that this fact invalidates the bug report than you are drawing the wrong conclusion. It is one thing to not support HD texture packs, but this BUG is actively blocking the use of them.
Just try to see it this way: Is this intended behaviour? IF no then BUG