Could you post your shader code if possible? If not, I'm just guessing that maybe your shader is using code newer than shader version 410. Try increasing the shader version number in your shader and see if that helps.
Even if I use a very simple vertex shader, it still show that "warning,version 410 is not yet complete;most version-specific features are present, but some are missing."
Such as the following vertex shader:
uniform mat4 mvpMatrix;
in vec4 vVertex;
gl_Position = mvpMatrix * vVertex;
But when I change the version to 140 or 130, the warning is gone. And when I change the version to 120 or 110,it shows that the version don't support gl_ClipDistance.
In my shader, I used variable array that the version 140 don't support, so I have to use newer version.
That's just the reference compiler informing you that not all language features of ver 410+ are available for validation. It will try and check what it knows about, only. You'll get the same warning on NVidia and Intel cards as well.
The shader issue you are having on AMD is real (see the clip distance thread on the forum for more details), but the warning is nothing to worry about. I'm using it with 430 and 440 shaders.