Common problem. The old flashers seem to take so much power that there's none left for the ignition. Mine had the same problem and was fixed by replacing the flasher with something like this.
http://www.ebay.com.au/itm/LED-Flasher-Relay-FAST-BLINKER-FIX-Plug-and-Play-for-Most-Motorcycles-ELFR-1-/180852014120?pt=Motorcycles_Parts_Accessories&hash=item2a1b9ebc28
Mine is a 12v one too but works fine with 6 volts.
Also worth checking all the connections in the indicator circuits as poor connections may also be drawing current.