How are the heating pads/flex-watt for each rack connected together, or to the thermostat? (In regard to series, parallel, or combination)
If they are connected in series the current will be the same through each and the heat output should be the same.
BUT if they are in parallel there is a chance of the current differing in each rack due to slightly differing resistances in the heat mats/ flex-watt. This could cause the heating elements in each rack to output a slightly different amount of heat like you are describing.
if the two racks are connected in parallel it might be worth measuring the total resistance of each heating system with an ohmmeter to see if they are the same or different. If they are in series this probably isn't the problem.
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