I'm confused by your statement, "the charger started its blinking lights ordeal indicating it was charging correctly, and thus not charging."
Does it charge or not? Is this true for both batteries? What exactly happens? Do you have a voltmeter to test the batteries and the charger?
Both original batteries don't charge (including the new battery I made, thus all 3 batteries don't charge). There is a little reset button on the charger that I have to press in order for it to kick start its cooling fan, and it will only run with the fan while trying to charge one of the batteries. The other battery it doesn't respond at all to. Nevertheless, the light that blinks and is supposed to remain steady after 5 seconds never quits blinking; thus indicating an error. It says to refer to the [owner's] manual if blinking exceeds 5 seconds. The bike didn't come w/ a manual, but I was able to get a pdf version e-mailed to me from the friendly folks at Giant Bicycles. The manual says to bring the bike into your dealer, HA! I have tested the batteries and they all have a charge of approximately 37-38V, but I read on another forum that they need to bee at least over 39V preferable 40-41to get the bikes SOC indicator to give a healthy read out and for the bike to function properly. I haven't tested the chargers volts, as I'm unsure how to. I can't help but wonder if there isn't a problem w/ the little resistors, or temp sensor, hooked up to the battery, and thus causing the error w/ the charger. I disconnected them from the pack I made (soldered) after initially connecting them to it, to see if that might appease the charger, but still no dice.
Again TIA for any help.