STM32F407 - ADC in Scan mode setting overrun bit
I have same problem with my stm32f405. I find next text in errata :


  When a software start of conversion is used as an ADC trigger, and if the ADC_SQRx or
  ADC_JSQRx registers are modified during the conversion, the current conversion is reset
  and the ADC does not automatically restart the new conversion sequence. The hardware
  start of conversion trigger is not impacted and the ADC automatically restarts the new
  sequence when the next hardware trigger occurs.


I think u solved this problem how ST-designers advised.