Ahem, it is entirely possible that the rangefinder of your M5 is a tiny bit decalibrated. Absolutely do check with your M3, too. If you get the same misfocus, then yes, most likely your lens is out of spec. COULD be in spec though and both your rangefinders out by the same amount 🙂
I lived with a lovely collapsible Summicron that frontfocused by 1,5 - 2 centimeters... you quickly learn to focus and "lean in". That said, nothing beats a rig that focusses exactly where it should.