2.7T All-Road won't start
 

2003 All-Road, 2.7T, six speed. I let the battery get low, recharged it in the car, it cranks over fine, but will not start.
It was running fine until it sat so long the battery died.
The check engine light is flashing, the EAP light is on steady. I let it sit for 20 minutes with the key in the ON position, then tried, no change.
All key functions work, all accessories in the car work. Cranks fine, no start.
Any thoughts?

Just a quick update to this, I finally replaced the battery with a new one, even though the old one tested good after recharging. I used the ignition key to manually lock and unlock the drivers door. After that, the car started right up.

Dave