Smoke after the kart is at speed is NOT normal. It is possible the jetting is way too rich. Do you know what your current jetting is? You should have a main jet of 160 in it at these colder temps. If your jetting is correct, the next thing to check is the amount of oil in the mix. The Rotax should be at 33 to 1. Do you shake your fuel tank after it has been sitting? Most oils, particularly caster oils, will separate from the gas particularly at these cooler temps and you will get a heavy dose of oil at start up. Before running your kart, shake it vigorously to mix the gas/oil. If you are using a castor oil, switch to Motul 800 synthetic. It will stay in suspension better.
If it still smokes after all this, it most likely is a water leak of some sort. Have you checked your water level in the rad? Does it go down over the course of the day?