(edit: ignore this post; since the AMD driver didn't optimize out the input attribute it obivously works)
First I thought, that this is an Intel bug, therefore the repro sample's name is "51_IntelBug". But it turned out, that the Intel driver was right.
What I'm doing is very simple: I use a shader with a VAO where certain input attributes are disabled (it relates to caching VAOs, but you don't have to deal with that).
Repro source code: Dropbox - AMD_hidden_bug.zip
The point is, that you shouldn't see the 4th quad, as the gx_TexCoord0 attribute was never enabled in that VAO.
On my R7 360 I see it (bug!!!), while on the Intel HD 4600 and 530 it's (correctly) invisible, as the vertex shader doesn't fetch the texture coordinate (instead fills it with zeros).
This is the INCORRECT image:
Could you provide the binary of your program?
I want to test it out on Linux. (I know you uses Windows API in the code. I'll run it with WINE)