Mosfet is getting hot under 3v drive
The answer to this is fairly simple. The MOSFET turns on more (i.e. to a lower drain to source resistance) when it is given more gate voltage. In your case the 5V gate drive was letting the FET go to lower resistance than what you are now getting with the 3.3V gate drive. At the same load current this increased FET resistance is causing more heat to be produced in the FET thus they get hotter.

BTW.....the 1V level that you mentioned is not the instant threshold where the MOSFET goes from Off to fully On. The MOSFET has a range of voltage on the gate over which it turns on.