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I had that problem with 2 different headsets on my S3. I never did find a solution but it only happened 2-3 times a week. I know that's no help but thought I would throw it out there.
Alot of car manufacturers are picky about what devices are supported and which are not. Do you know if the s3 is officially supported by the stock HU in your Civic? Have you tested out your bluetooth with any other devices? Does the s3 connect via bluetooth to other devices flawlessly?
Wife and I each have the S3. No problem connecting to my 2012 Honda Civic. Do you have access to another Android for testing? I also connect to two different Alpines, MOTO headset, Plantronics and Blueant. No problems. I occasionally connect Bluetooth Direct to move pics/music to other Androids and tablets.
I have tried two different Galaxy S3 phones, both are a problem. They just constantly connect and then disconnect to the car's bluetooth. I also connected a Razr to the new Civic and it works fine.
I'm not too familiar with the new Civics, are you able to update the firmware?
I recall not too long ago a member having the same problem with a different make car. The dealership he bought it from offered to replace the whole HU for him and his BT issues were resolved. Maybe yours is faulty as well.
Since the vehicle is new have the dealership look at it. Be very specific. Most of the info you tell the front person will not get passed to the tech. Found this out while troubleshooting a bad microphone on my 12' Civic. Dealership called to say no problem found. Once they put me in touch with the tech the problem was easily diagnosed.