You might try putting a 100 uF capacitor across the clock power wires. Install the capacitor as close to the clock as possible and be sure that its rated for at least 15 volts and that you observe the correct polarity. The capacitor will smooth out any transients.
The old style clock will set off the alarm when the magnet resets itself. The alarm sees the voltage drop in the system the same as opening a door and the dome light coming on. The quartz conv. should fix it. I would try the heavy capacitor also. That might fix it. The magnet has a fair amount of current draw.