Yes...but sadly it isn't available just yet. The CTRIO2 due out in a couple of months does this beautifully, at up to 250k.
In the meantime, I honestly don't know of any good way to fix it. The CTRIO was not really designed for pulse output, and it was no small feat to make it work as well as it does. The suspend function is admittedly dang near useless. How's that for honesty?