That's interesting. It might be to do with the frame change around 2002?
Is your battery upright with the terminals at the top, or does it lay down like the S4?
If so it might be more to do with the revised airbox, possibly?
Now you've got it sorted, it's a very good time to closely inspect the connections and cable condition of the three Yellow cables from alternator to reg/rec.
It's very important that the connections in particular are of low resistance. In other words, very clean, tight and conducting as well as possible.
Corrosion or looseness will create resistance and heat which will melt the connector and cable insulation. It will destroy your regulator, could boil the battery and it has been know to start a fire!
I had a close call with the standard plastic connector block, which had partially melted and the cables where locally scorched.
Luckily I do regular inspections and caught it.
I now use Gold connectors on those three connections, as I have done ever since on all my bikes.
I use 4mm Gold bullets available from model shops for RC aircraft and cars and inspect annually.
Others hard wire, or use tubular crimps.
If you're really a worrier, you can fit a battery monitor/charge warning light like this.
This gives you Rubber wrapped construction for waterproofing and shock resistance. A Shallow Installation of only 29mm depth behind your panel surface. Integrated tri colour (Red, Green, Yellow) 10mm LED and microprocessor assembly.
www.ebay.co.uk
It was one of these that saved the day when the (new) reg/rec failed on my Commando.
There are some different versions.. The choice is yours..