That sounds very strange indeed. I forgot to add that I'm on Unity Pro right now.

I tried two different ways of creating a new shader,

right-click >> create shader

Open the shader in mono develop and paste the code from pastebin

Open shaderforge and create new shader, save and close.

Open the new shader in monodevelop and paste the code from pastebin

Both list all my possible inputs in the Inspector but none of them has any connections when I open them in shaderforge

One of these new shaders applied to one of my meshes produce a working result but when I open it in shaderforge again and compile it breaks.

Here it is:

http://pastebin.com/HEAUYwU5

I'm running 4.2.1f4

Maybe it's not actually related to the duplication as opening yesterdays working shader shows a now broken one. But some of my shaders have kept their connections.

What are you referring to when you say new shaders? I have yet to run into an instance where it doesn't occur. If you are thinking of shaders from previous projects, or from older versions of ShaderForge I can't say. As I've just started using your software I can only talk of my current project.

No, there was no tessellation or displacement involved. I even copied the non-working shader onto my desktop to save it from this, but that did not seem to help either.

If I can provide you with any other kind of help please let me know! Or if you want me to do some kinds of tests.

A short follow up. This duplicaion seems to have contaminated the shader. No connections are stored in my shader any more. Every time I open it there are just nodes, no connections.