To reproduce:
1) Open attached project
2) Notice that there are 7 textures. Some of them have override for standalone enabled, some disabled. Also they have varying other properties
3) Select them all
4) Notice that options like "Alpha from Grayscale" get a "-" to indicate that not each texture has it enabled, yet override doesn't show that (sometimes it shows tick, sometimes it shows nothing. Seems to be dependant on whether first selection is overriden/not, but it seemed random).

Screenshot of this: http://i.imgur.com/prnvz1W.png