Well if you are experiencing this noise when you start your car in the cold, the idle is usally quite a bit higher, and then lowers back to normal rpms after a few minutes. So this might not be alternator noise, it could be some other engine noise.
Also are you saying you have two batteries, or that your main battery is mounted in your trunk ?
If so, how is it / where is it grounded?
If its a tank battery how are they connected?