1. I have never had that problem.
2. First you must understand that there are Materials and there are Colors/Textures (that might be named like the materials they represent, but have no physical properties like Density...).
Materials, like Aluminum, might also be assigned a color/texture - like maybe cast, brushed or polished aluminum or maybe just "aluminum".
Now that we have established that there are both materials and colors/textures named like materials we must understand that there are several ways of assigning these materials or colors/textures (remember - two different Properties).
Material properties are normally set by right clicking on the top node of a part at the part level and selecting iProperties and then Physical and set to desired material.
Colors/textures are normally set by right clicking on the top node of a part at the part level and selecting Properties.
But colors/textures can also be set at the feature level by right clicking on the feature (for example right click on a Hole feature and set it to some shiny color/texture to cosmetically represent machined feature).
Individual face colors/textures can also be changed by right clicking on the face and selecting Properties.
All of that was at the part level.
It can also be done at the assembly level - without effecting the part at the part level.
For example, you might sell the same machine painted red, blue or green. The part level isn't painted.
But at the assembly level it is. You create each variation and then create a View Representation of each variation.
The same for materials.
You might want to run FEA (Finite Element Analysis) to test the strength of an assembly, but don't want to set the material in the part until you have made a decision on what material to use. At the assembly level you set the material (like steel or aluminum), run your test and then set your part material based on the analysis.
All of this might seem quite confusing at first, but once you get the hang of it - it all makes such logical sense in relation to the real world that you wonder how it was ever confusing. The key in Inventor is to think like you are working with real world physical parts unlike in AutoCAD where it allows you to violate all sorts of logic that isn't possible if you were doing the same thing with real parts out on the shop floor.