I found the problem: 

if KC0[0].x == index (=0):  

1      x: ADD_INT            T0.x,  KC0[0].x, [0xfffffffe -nan].x
2      x: MOVA_INT           __.x,  T0.x

Address register is now -2 and hence,  in the next step R1 is unconditionally
written, and this is actually the gl_Vertex value ...

3      z: MOV                R[3+AR].z,  0
       w: MOV                R[3+AR].w,  [0x3dcccccd 0.1].x

that is here used to evaluate the gl_Posuition. 

5      x: MUL_IEEE           T0.x,  KC0[1].w, R1.x
       y: MUL_IEEE           T0.y,  KC0[1].z, R1.x
6      t: MULADD_IEEE        T0.y,  KC0[2].z, R1.y, T0.y   SCL_212
...

In the un-optimized shader R[3+AR].w is only written to if (KC0[0].x >= 2), and
hence AR >= 0;

I.e. the sb optimizer is to aggressive in optimizing away the conditional
blocks.