If the battery warning light comes on after 30 secs,then the system is charging in default mode,and thus the smart charge system is not working correctly.This could be an alternator or wiring fault.There is a procedure for checking the system properly.

Hopefully the new battery is the correct calcium type,otherwise the smart charge system will not perform correctly as voltages can peak at around 15.8 volts.If you have a digi voltmeter,then you need to check the voltage at the battery and at the large terminal on the back of the alternator.These should be approx the same.Next,disconnect the 3 pin connector at the alternator.and check voltage on the red/orange lead .Again ,this should be the same as the battery voltage.Do this test engine off. now you need to load test this small red wire with a 21 watt bulb to see if it lights up.If the tests prove good so far,then i would say the alternator is in trouble.It is possible to test the other 2 wires in the plug(blue and gray)but you will need an oscilloscope.Finally,you need to remember that the red battery charge warning light is not connected to the alternator.

just stripped alot of the alternator 3 pin loom out

Found that the blue wire connecting to the plug looks a bit dodgy not broken but is twisted and stretched could be why the battery lights coming on 30 seconds after start up

Can you buy this part of the loom seperate or even the plug and re solder the wires back up

Any help here would be appreciated

thanks