Why are node groups not being saved in my startup file? I made four node groups in blender and saved the blender file to my hard drive. I want these node groups to appear every time I start Blender, so I do have not append them every time I need them. So I opened up a new blender file, clicked on "append" and appended all of the node groups from other blender file. I click on save start-up file and exit. When I open blender again, the node groups appear but not all of them. Only one or two. if I append the missing node group again, and save it again, the next time I open up blender all node groups are gone. It is like random.

Am I doing something wrong or something is broken with blender?
Node groups have users linked to them, like materials or textures. If a node group has no user, it will not be saved to the blend file. After startup they will be gone. In some cases it takes more than one restart and save before all unused instances are gone due to internal dependancies. 

You could, as aliasguru suggested, set fake users. This could be done by executing this line in the python console:

for node_group in bpy.data.node_groups: node_group.use_fake_user=True


Afterwards they should not disappear anymore. Note that you have to repeat it for every file and when you create new node groups.