How to configure Multichannel ADC properly? Currently two different values stored in same variable
I don't know if you solved the problem, but as I see, you need to change 

AdcHandle.Init.EOCSelection = ADC_EOC_SEQ_CONV;


to

AdcHandle.Init.EOCSelection = ADC_EOC_SINGLE_CONV;


Because, ADC_EOC_SEQ_CONV flag is rised after the all conversions are ended (all channels passed), but you need move data from the ADC to the memory after each conversion, so use ADC_EOC_SEQ_CONV.

If it doesn't help, can you please post your DMA configuration?