Index: release/scripts/startup/bl_ui/properties_material.py
===================================================================
--- release/scripts/startup/bl_ui/properties_material.py	(revision 38485)
+++ release/scripts/startup/bl_ui/properties_material.py	(working copy)
@@ -174,6 +174,7 @@
         row.prop(mat, "use_transparency")
         sub = row.column()
         sub.prop(mat, "offset_z")
+
         sub.active = mat_type and mat.use_transparency and mat.transparency_method == 'Z_TRANSPARENCY'
 
         row = layout.row()
@@ -199,6 +200,7 @@
         col.prop(mat, "shadow_cast_alpha", text="Casting Alpha")
         col.prop(mat, "use_cast_buffer_shadows")
         col.prop(mat, "use_cast_approximate")
+        col.prop(mat, "pass_index")
 
 
 class MATERIAL_PT_diffuse(MaterialButtonsPanel, bpy.types.Panel):
@@ -729,7 +731,8 @@
         col.prop(mat, "use_vertex_color_paint")
         col.prop(mat, "use_vertex_color_light")
         col.prop(mat, "use_object_color")
-        col.prop(mat, "pass_index")
+        if simple_material(base_mat):
+            col.prop(mat, "pass_index")
 
 
 class MATERIAL_PT_shadow(MaterialButtonsPanel, bpy.types.Panel):
Index: source/blender/nodes/intern/SHD_util.c
===================================================================
--- source/blender/nodes/intern/SHD_util.c	(revision 38485)
+++ source/blender/nodes/intern/SHD_util.c	(working copy)
@@ -83,7 +83,11 @@
 void ntreeShaderExecTree(bNodeTree *ntree, ShadeInput *shi, ShadeResult *shr)
 {
 	ShaderCallData scd;
-	
+	/*
+	 @note: preserve the material what was hit, this will be pointer will be modified by the shade tree
+	 fix for bug "[#28012] Mat ID messy with shader nodes"
+	 */
+	Material* mat = shi->mat;
 	/* convert caller data to struct */
 	scd.shi= shi;
 	scd.shr= shr;
@@ -92,7 +96,8 @@
 	memset(shr, 0, sizeof(ShadeResult));
 		   
 	ntreeExecTree(ntree, &scd, shi->thread);	/* threads */
-	
+	// @note: reset the material to original hit
+	shi->mat = mat;
 	/* better not allow negative for now */
 	if(shr->combined[0]<0.0f) shr->combined[0]= 0.0f;
 	if(shr->combined[1]<0.0f) shr->combined[1]= 0.0f;