I had a similar problem during my Mun mission. Near as I can tell, the heat generated by the ISRU is burning off your heat shield, which is kinda silly. Apparently heating is getting some tweaks in a coming patch, but until then, don't put your heat shield right against your ISRU and be sure to add some parts like wings to the parts around it to dissipate heat. Also, an engineer is supposed to reduce overheating, but i'm not sure it would help in this case.