Note: All testing was done WITHOUT any mods being installed
In 1.9 a new thing was added that allows you to change textures on items based on their damage variable, for example if I have a wooden sword that is not damaged, I could have a texture, and then if I have the same sword 25% damaged, I could have a completely different texture. However using forge I am unable to see the version of the damaged texture, as I can on vanilla. So if I have one resource pack, it will work fine with this on vanilla, however not on forge.
For more info on damage variable textures here is a link to a youtube video that describes them well.