I would check the wiring to the flipper coils and the EOS switches. It sounds like something was reversed when the new coils were installed.

The driver board only enables the flipper circuit through a relay. And the relay either works or it doesn't, never seen one cause the fuse to blow. If the transistor that controls the relay was shorted on, you would have flippers all the time.

Take your multimeter and measure each coil, like a poster said above just because the coil is new doesn't mean it isn't bad/shorted internally.