Performance Monitor % Processor Time metric difference between _Total and sqlservr.exe
The Process: % Processor Time (Instance - sqlservr.exe) counter takes into account all of your cores. If you divide by the cores you get an answer much similar to what you expected.

This TechNet article explains it in far more detail but it uses this calculation to get the number you see:
(No of Logical Cores * 100),  So this is going to be a calculated over a baseline of more than 100.