I tried two test cases to see if I am also able to produce. I have two installations on my system for Kentico. One is Kentico 8.2 and other is 9.
Test 1 - Ran CodeUpgrade "Path to Solution file" for Kentico 9 using tool. I got same error as yours.
Test 2 - Ran CodeUpgrade "Path to Solution file" for Kentico 8.2 using tool. The tool ran successfully.
I am not sure if it will really work, can you try putting your path inside double quotes and see. This seems more of some internal exception.