While out for a ride today after stopping at a junction the ar started running rough. So stopped and switched off and started it again. When it wa ticking over I noticed that the neutral light was pulsing(flashing) in time to the engine tickover. I also noticed the indicators had stopped.

Electrical problem, check your reg/rec output as a start

+1

It is brand new

No. Connection problem possibly, false earth or generator fault?

Bad Earth Doh!!

like I said love/hate with these things.

Next why is the high beam indicator light glowing all the time?

all signs of earth problems.
Take a weekend out to go over every plug and connection on the bike.

Check all connectors are clean and plugged together properly