try redownloading the pack it sounds lie something in the download got corrupted.I have a problem where Thaumcraft Textures are missing for the most part. I can't seem to find a solution. I haven't changed anything but just downloaded the pack and away I went. Example. . . Iron capped wand shows a gray stick. Many other textures are just white squares in Thaumcraft.
EDIT: Just saw that Reliquary is another mod that has mostly missing textures.
Any ideas why this is happening?