Please check the actual amplitude of the gate voltage pulse applied, using an oscilloscope. If the amplitude is low, the MOSFET moves away from saturation and hence has higher heat generation. This is a problem on high side only since usually such power supplies are either separate or are derived through "bootstrap" techniques from the low-side. The pulse amplitude must be above 10volts.
My friends, please note that Shiva stated that only the high-side MOSFETs get hot. Thus, it cannot be due to slow switching or due to HV MOSFETs, as then all MOSFETs would be hot !