'06 Zephyr Key Fob No Ignition

Bit of a strange problem here. A while ago, the battery on my keyfob remote went dead. I've recently put a new battery in it. I can lock/unlock the car, however when I put the key in the ignition and try and turn the car on, it will not start. My other key works fine.

To make matters even worst, since reprogramming this keyfob, the keyfob that won't turn on the car, is actually unlocking/locking the car doors to our Ford Focus 2012. One of the keyfobs on the Ford Focus can unlock/lock the Zephyr as well as open the trunk.

Is there anything I can do at home to fix this problem?

The dealership wants $125 to "diagnose" the issue. I believe it would be over $100 to reprogram each set of key. Oh and they cannot promise that the Ford Focus keyfob won't still be able to lock/unlock the Zephyr.

Hopefully someone out there can help!