I don’t think 40c is going to soften the wax on your stone. Most likely you are running the machine far to fast and applying to much pressure on pre-polish, thus generating heat making the wax soft.
You can salvage the situation and carry on cutting the stone, using a BBQ lighter and the machine dial gauge.
Use the lighter to heat the dop enough to soften the wax and straighten the stone up by eye. Put the dop back in the chuck and set the machine to 90deg, rest the stone on the lap and using the dial gauge find the highest spot on the stone. Gently heat the dop with the lighter and press it down, noting the dial gauge position. Rotate the stone round to the new high point and repeat the heating process, eventually the stone will be central on the dop.
Recut the stone.