I've run into a few motherboards that don't work well with Uniflash. It wouldn't surprise me if those same boards don't work well with other generic flashing utilities either. So you might just be unlucky with the particular motherboard you're using.
There are also cases where a particular type of Flash ROM just doesn't work on another particular board.

Be careful with voltage mismatch. 5V and 3.3V PLCC Flash ROMs are both common on motherboards. If you put 5V into a 3.3V chip it will be destroyed. If you put 3.3V into a 5V chip, I would guess it just won't work right. You can check the power supply voltage either by finding a datasheet for the chip's part number, or just by probing the pins with a multimeter while the board is running.

DIP chips on motherboards are almost always 5V, but even those boards sometimes have jumpers to select an alternate voltage setting (I think 12V with those). So to be really safe, you should check that the voltage matches even for DIPs.
Ideally, if you have a datasheet for the chips then you should also check that the power and ground pins are in the same places, but I don't think I've ever run into a case where the pinouts had a dangerous mismatch, just the voltage.