Repro steps:
1) Open the project and AmbientOcclusion.scene
2) Notice four spheres in it - only one - 'DoesWork' shows Ambient Oclussion text on the sphere
3) If you open ShaderWorking.shader, you will notice, that the o.Alpha is dependent on Texture2.a and UV2 set
4) If you open ShaderNotWorking.shader, you will notice, that the o.Alpha is equal to the Alpha of the first texture and thus, is not working

Workaround: use 2nd UV set's data

Reproduced in: 5.4.0b3; 5.3.2p1; 5.2.3p3; 5.1.4f1