I don't know whether anyone is reading this thread still, but I have the same problem. I'm texturing a poly object to which I've applied a cylindrical map using Edit Polys>Texture>Cylindrical Mapping. My material has a colour map, a bump map and a specular colour map. All three channels line up perfectly in the default UV set, but when I apply the set created by the cylindrical map, only the colour and specularity channels show up for linking in the UV Linking editor. Consequently, I can get the colour and specularity maps lined up where I want them, but I can't position the bump. I've tried manually linking the UV Chooser to the Texture Placement node of the bump channel, but it has no effect, even though it is the same one that is linking the other channels. If I apply the bump map to a different channel it will line up fine. The problem seems to be with the Bump2D node, and I can't at present find a way round it.
Don't know if this explanation helps in tracking down the problem... or finding a solution.
yeah i tried lowering the bump map depth and no alpha channel is required.. but what i would like to see is JulianBT's maya files, or model, and maps to see if we can compare to see where we might have the problem. Well hopefully you'll read this and post your stuff.