I think i am able to relate to your issue. Couple of months back my TBTS 500 started to face a similar situation though not exactly the same. I was getting a Low batt indicator light when my bike was not even an year old. Soon, the battery go totally discharged. So i got it replaced under warranty. After about 2 days, the problem once again came back on a brand new battery.
So this time i shot a mail to RE people giving them he proof's and telling them what a shady job the SVC people had done. My bike was then called in for inspection and the mechanic told me that the alternator had gone kaput! So that had to be now changed under warranty. After the alternator was changed, my bike had no issues.
Still, when i switch on the bike, the low batt indicator is there for like about 5 secs and then its gone. I can also feel that the batt gets under too much stress when i self start the bike.
I am guessing that the problem in your bike too lies in the wiring (electricals) which is causing your batt to malfunction. I suggest that you get it checked up at a good SVC thoroughly.
Cheers




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