Altera example matrix multiply produces Compiler warning: non-vectorized load/stores

That warning is related to global memory accesses and is normal when SIMD is used. If the compiler fails to fully coalesce such accesses under the presence of SIMD, it will generate that warning. What it is trying to say is that don't expect to get linear performance improvement by using SIMD, if your global memory accesses are not contiguous. However, if your kernel is memory-bound and you use SIMD despite accesses not being contiguous, performance will actually go down.