To reproduce:
1. Create a few standard materials (I'm using 3)
2. Apply the materials to some cubes in scene
3. Multi-select the materials in project view
4. Change the Rendering mode to transparent and change the diffuse alpha value - notice that only one material changes (the other materials are not set to transparent)
5. Change the color value of emission - only one material is updated
6. Set the texture of the Detail Diffuse x2 - only one material is updated

Note that the settings get changed for all of the materials (except for the rendering mode setting), but visually they can only be seen on one. Thus the other materials remain in a broken state until they are updated manually.