Then I found out that this is one of the problems with the Nexus 7 when it is upgraded to 4.2.1 Jelly Bean. When the Nexus 7 battery runs completely out, it sometimes refuses to charge at all. What you are seeing is the device chucking a tantrum. The device is in sleep mode and you need to get it completely off in order for the device to charge. Without these tips, I am sure you would never have figured it out, so this is what you do;
1. Unplug the charger. Hold down the POWER and VOLUME DOWN keys simultaneously and with the other hand somehow plug in the charger. If this works, there will be a large boot screen that will appear.
2. Press the Volume Up button until you see the option POWER OFF DEVICE
3. Press the POWER Button to select this option. The device should now switch off.
4. Unplug the charger and then plug it back into the Nexus 7. The battery charging icon should appear if you were successful.