Hi there. I too have had the same problems with my bike. I know it's been a long while since you posted, hopefully, you've fixed the problems. If not here's what I did. Everyone else is right,
First get yourself a multi-meter & see what you get for a reading. New battery should read a solid 12+V. if not charge the battery.
Second, with the bike running, take another reading, you should be getting between 13V & 14V.
Third, Turn the bike off, take the key out. Disconnect the NEGATIVE battery lead. Place the NEG terminal of your meter to the NEG post of the battery and the POS terminal of the meter to the NEG battery lead. Your reading now should be .1 or less. If it's any higher, you've got whats known as a "static drain". To find the drain, with the meter still connected (you may need an extra set of hands) start pulling the fuses one by one. When the reading drops to .1, there's your problem.
The last thing I checked was my Regulator/Rectifier. Now this is a pain in the ass to get to because it's under the fuel tank.
If all of these things are working properly, then yes it's you charging system.