I hear this one a lot. The way the original power supply (PS) is wired is somewhat goofy. The coin door and control panel (CP) get their ground from the original PS header 4J3 pin 6. After installing your switching PS you probably disconnected the 4J2 connector from the original PS. By doing so, you now lost the games common ground for the coin door. Either one of these steps below will fix your problem:
A: Run a ground wire from your new switching PS to the original PS header 4J2 pins 7-10. You can plug in the original plug 4P2 into 4J2 and cutting all wires except pins 7-10. Make sure you still have the header 4J3 connected to the original PS
B: Or you can run a ground wire from your new switching PS to the coin-door. Just make sure your CP is also getting the same ground.
Step "A" is probably the better of the two if you're still using your original PS transformer as isolation to the monitor and want to power the lights on your coin-door, which use the 4J3 header pins 1 and 2 on the original PS.
Below is the a PS used in Defender game:
Below is the newer PS used in games like Joust, Robotron, Stargate and Sinistar and a few more: