In some cases i also had the impression that CLR code (C#, ...) runs actually faster than a fully optimized C++ program. I can't remember exactly what it was, but it was about a simple algorithm.

If you have an allocation-heavy program that runs rather short, a CLR program will outperform the C++ variant, because garbage collector is trimmed on allocating a really huge bunch of small and large memory.
(The above is an assumption i make based on my knowledge about memory allocation)

Also i don't remember I/O beeing slow in C#. If you always read a single byte and convert it to hex, then print it to another file, this will be slow indeed....