Your comments

ah, nice! I'm looking forward to that release. Any ETA on it?
No errors when I open the window but when I modify a node that breaks ShaderForge I get errors.
It's spamming the console with these two errors at that time:

Red Warning:
NullReferenceException: Object reference not set to an instance of an object
ShaderForge.SF_Node.GetInputData (System.String id)
ShaderForge.SF_Node_Arithmetic.IsUniformOutput ()
ShaderForge.SFN_If.IsUniformOutput ()
ShaderForge.SF_Node.Draw ()
ShaderForge.SF_EditorNodeView.OnLocalGUI (Rect r)
ShaderForge.SF_Editor.OnGUI ()
System.Reflection.MonoMethod.Invoke (System.Object obj, BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) (at /Applications/buildAgent/work/c514da0c8183631c/mcs/class/corlib/System.Reflection/MonoMethod.cs:222)

Yellow Warning:
Attempt to find input node of connector B of Multiply
UnityEngine.Debug:LogWarning(Object)
ShaderForge.SF_Node:GetInputData(String)
ShaderForge.SF_Node_Arithmetic:IsUniformOutput()
ShaderForge.SFN_If:IsUniformOutput()
ShaderForge.SF_Node:Draw()
ShaderForge.SF_EditorNodeView:OnLocalGUI(Rect)
ShaderForge.SF_Editor:OnGUI()
UnityEditor.DockArea:OnGUI()
Installing the new 0.14 version in the project did the trick! It even looks like most of my old shaders are loading too. Thanks for your quick response Joachim!
I see and fully understandable! I guess I have to take the plunge to 0.14 then.
Thanks for letting me know.

So, I've been lying a bit. My files weren't readable at all. The tickbox for the skybox's readability was hidden due to a somewhat smaller inspector pane (great work in usability Unity!).

So the bug is understandable now, the connections are lost once a file isn't readable.

Recreating the same exact shader in shaderForge but leaving all the input nodes empty creates a shader that has no problem whatsoever.

However when I specify that the Night cubemap should load inside of shaderForge it breaks. But the previous shaders that have no inputs specified are still working fine.

I don't seem to be able to change the readability on the individual faces of the cubemap. The textures linked to the cubemap have no such setting either and the files in windows all have correct read/write attributes.

Yes, actually I did (still learning to check all the places in unity):

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UnityException: Texture 'Night' is not readable, the texture memory can not be accessed from scripts. You can make the texture readable in the Texture Import Settings.

UnityEngine.Cubemap.GetPixels (CubemapFace face) (at C:/BuildAgent/work/cac08d8a5e25d4cb/Runtime/ExportGenerated/Editor/Graphics.cs:1054)

ShaderForge.SFN_Cubemap.RenderToTexture ()

ShaderForge.SFN_Cubemap.DeserializeSpecialData (System.String key, System.String value)

ShaderForge.SF_Parser.ParseNodeRow (System.String row)

ShaderForge.SF_Parser.LoadFromNodeData (System.String data)

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This Texture, Night is a skybox but has Readable Ticked so I don't know why it's like that?

The attributes of the file are correct too, no read-only attribute in windows either.