I think this is all related to the engine trouble warning light thing. Anyway got a new battery recently and it was fine. Then it lost its charge so I fully charged it and it was fine for a few weeks. Now it has gone flat again. I already changed the rectifier so it's not that. Any ideas guys?

Does the bike have an alarm system? Have you added anything to the system?

Check and clean all connections, and for loose connections

I had a not disimilar problem on my old radian a few years ago. Rigged up this led unit so that I could see what was happening while riding. Worked a treat. Took it off once I bottomed the problem, must still be in the sanctuary somewhere. Easy to wire in, bit of imagination to mount

Whats your commute Grouch? A couple of miles each way with lights on will not be enough to top up the battery

Was the replacement battery the correct one with the same Amp Hrs as the auld one

Have you got a multi meter, if so test the battery it should read about 13v (assuming it is a 12v system) and then start the bike up. It should rise to about 14v

If there is no multi meter, then fire the bike up put the lights on and raise the revs, you should see the light get brighter

The above will give you an indicator whether the battery or the alternator is goosed

Kind of basic advice, but enough to get started with

All the above are great ideas Grouch but have you just tried riding to work with the lights off? maybe just side lights, see if that makes a difference.

Cheers guys. I only do a few miles each day but every day I do at least a few miles. I can't turn the light off on newer models the dipped beam (I think that's the name) is permanently on. I will test it tomorrow with my multimeter. I really hope it's not the alternator, that sounds expensive haha. I suppose I will have to just charge the battery once a fortnight or whatever. I never thought that I was not riding enough to charge it. 

Take the long way home Grouch it's the perfect excuse