one thing that I've noticed is that by simply applying a map to the transparency of a material, it doesn't apply the texture's "color" to the transparency, but the texture's transparency to the transparency, which isn't exactly what you typically want.

In order for it to appear correctly, I have to manually link a texture's out color to the material's transparancy. After that, if I turn on High Quality rendering, the transparancy shows up properly in realtime.