Oh wow, really?
That sounds like something on Unity's end. Do all shaders get this or just those specific ones?

That's very strange. What errors are you getting in your console?

What version of SF are the shaders you're trying to open from? Sounds like they're either really old or you have a strange window layout saved.

Also, try this reinstall method:
http://acegikmo.com/shaderforge/faq/?Q=erroronnewversion#erroronnewversion

That's most likely why. If you're on Windows, Unity defaults to DirectX, but you're not compiling any DX compatible shaders. Just check d3d9 and it should work on all machines again :)

Do you have d3d9 in the shader as well, in addition to the OpenGL ones?

Is this for all shaders, or does it only happen with specific settings?
For instance - if you insert a red color into Emission, and set the shader to Unlit, does it work?
If you input red into Diffuse, and set it to blinn-phong, and set it to only receive a single directional light, does it work?

Also, any errors or warnings in the console/logs?

Are you using the same platform? Are you using the same quality settings?

It's just the node preview that's showing up like that. I guess the issue is two fold:

1. The Texture2D node cannot simply always apply the alpha channel to all textures, as you often use the alpha channel for something other than transparency, such as specular masking, etc.
2. In this case, SF should apply the alpha to the node preview, if and only if you've marked the node to use the alpha as transparency. However, last time I tried this, it returned incorrect values, so it was unreliable.

Generating .cginc files with SF seems a bit redundant, given that nested nodes will give you more or less the same functionality. But yeah, being able to include them is a good idea, and I'll do that at some point :)