IWT in ISBoxer usually disables CTM as part of its normal setup. This is on purpose, because of broadcasting mouse when the toon perspectives are never 100% exactly the same might mean you end up with toons running around the place. On the other hand, IWT also turns on CTM as part of it's process.

You could emulate this same behaviour in your own mapped key. Check out the ISB42 - Party -> IWT Standard mapped key for how to set this up.