It certainly sounds like the EOS switch not opening fully when the flipper is 'up'. Remember there are 2 switches on the flipper bracket. One should open, that's the high power to the flipper which would then just leave the hold power. The other switch should close and that's the one on the switch matrix which the game uses for triggering lane change etc.
Can you throw here a few pictures of the wiring and switches? Sometimes a second set of eyes provides that "D'oh moment"...
Mark