It took me some time to track the issue, it all came down to a stupid mistake i made while building the system. I will try to explain. The main bike battery and the 2nd battery are separated by a large solenoid witch is triggered by a time delay relay. when I added the time delay relay i had the 2nd battery supplying the 12 to activate the solenoid. When the 2nd battery drained past 12 volt it no longer had the power to trip the relay nor the solenoid. It was a very easy fix, just ran the 12 volt from the bike battery / charging system this way (as long as the charging system works) the 2nd battery will turn on the charge as it was meant to. Before i worked this out i have a feeling i wasted a battery or 2. clear as mud?