If it's only going to 2.5v, then you have a problem somewhere.
The IR2110's input needs to get up to 9.5v or higher, and the maximum input bias to get there should be 40uA.
You say that you are using 1k pull-up resistors from the output of the comparators to 12v. (12v-2.5)/1k = 9.5mA current. That is many times the current that should be needed to get the inputs higher.
Is your 12v supply for Vdd on the IR2110 staying at 12v, or is it dropping? How about the 12v side of the 1k pull-up resistors?
If it is staying at 12v, then try replacing the IR2110 IC.
The IR2110's input needs to get up to 9.5v or higher, and the maximum input bias to get there should be 40uA.
You say that you are using 1k pull-up resistors from the output of the comparators to 12v. (12v-2.5)/1k = 9.5mA current. That is many times the current that should be needed to get the inputs higher.
Is your 12v supply for Vdd on the IR2110 staying at 12v, or is it dropping? How about the 12v side of the 1k pull-up resistors?
If it is staying at 12v, then try replacing the IR2110 IC.