Issue with magsafe/charging (blinks green, amber, off)

Having a quirky issue with my mid-2009 Macbook Pro.
A month or so ago, I began having an issue with my macbook charging. When the computer is up and running and I plug in the magsafe it will say "Calculating..." and then say "Not Charging" and then switch to battery use. It constantly does this as long as the magsafe is connected. The lights on the magsafe will constantly cycle from green to amber to no light.
At first, it would do it a few times then it would start charging. Now it constantly does this without ever stopping. I was editing video the other day for a while and it never stopped the cycle.
Thinking it was the battery, I took it into the Apple Store last week and got a new battery because it had been saying "Service battery" for a while and the battery would only last about 20 minutes on a charge. So I just thought the battery finally refused to charge.
But the problem still exists.
The magsafe is new (only 3 months old) and here's the quirky thing: the computer will charge if it's asleep (lid closed) or shut down completely. No blinking lights at all. It will charge as long as it's asleep or shut down. So I don't think it's the charger. But as soon as you hit the power button to starting booting up, it will blink.
I have reset the SMC a couple times actually, but no change.
Is there something software/firmware related that I haven't tried? Any insight or suggestions would be greatly appreciated before I take it back to the Apple Store (which is about an hour away).
Thanks!

Try resetting the system management controller
http://support.apple.com/kb/HT3964?viewlocale=en_US
If that did nothing for you, try resetting the NVRAM
https://support.apple.com/kb/HT1379

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Thank you for providing so much information about what you are experiencing with your MagSafe adapter. I recommend reviewing the article below to troubleshoot this issue. You have already gone through some great troubleshooting steps, some of which are in the article, and you can skip those since you have already taken them:
Apple Portables: Troubleshooting MagSafe adapters
http://support.apple.com/kb/ts1713
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Issue with magsafe/charging (blinks green, amber, off)

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