The same network (Alexnet) has different performance number executing on FPGA for Caffe and ONNX input networks: the ONNX input is almost 35% slower. Executing on CPU the performance is the same.
It is caused by Reshape operator, that exists on ONNX and did not on Caffe. As I could see, this operator is not needed by Inference Engine, as alexnet IR from Caffe does not have it and run well.
My suggestion is to suppress Reshape operator on MO, as it is not needed.