Hello,
GPU Shader Analyzer is an offline analysis tool, so although it knows how the driver will compile the shader, it does not know anything about actual runtime performance. GPU PerfStudio measures the ALU instruction count based on what the hardware actually sees. In some cases, this may be slightly different than what Shader Analyzer reports.
Also, GPU PerfStudio 2.1 was just released with an updated profiler and now has DX11 and OpenGL support: http://developer.amd.com/gpu/PerfStudio/Pages/default.aspx