They are not purple, they are magenta (unless I assume wrong) and magenta is >9000 times better than transparent. This means they are magenta because they are using the default BLANK texture (instead of no texture at all) and can thus be fixed by applying the texture in the right place. Now, since i don't use HD textures and doesn't feel very motivated to install one of them all i can say is, try and figure out which file it is using and place some graphics in there.
But anyways, magenta is better than no texture at all. Now you know something is working as intended somehow.
Purple or magenta... so similar it doesn't matter in this particular case
And I don't know why you seem to focus on the HD textures - as it also happens with the DEFAULT texture pack.. (the one that comes with Minecraft..)
And I have tried adding the 3 pipe textures to various other texture files - and they just keep on being.. not there. Gah.