The EOS switches are not used in the flipper coil timing on these games. They are only there to provide an additional power pulse in the event of "flipper fold", which I have yet to see. Flipper fold is when the ball comes back so fast the the flipper drops. Maybe I never see it because I like to do drop catches. So the EOS cannot be a suspect here.
One thing not mentioned yet is the cabinet switch at the flipper button. They are low current switches, but they do wear out and cause this behavior. The flipper board has leds on it to show the state of the switches. Watch the board while pressing the flipper button. If the associated led only flickers, then you have found the problem.