Using injected ADC channels in parallel with regular conversions fails in ChibiOS on STM32. This is because
adc_lld_stop_conversion (os/hal/ports/STM32/LLD/ADCv2/hal_adc_lld.c) sets CR2 to 0 and then to ADC_CR2_ADON, resetting the injected channels bits. Proposed resolution: disable SWSTART bit, preserving other bits:
adcp->adc->CR2 &= ~(ADC_CR2_SWSTART);
adcp->adc->CR2 &= ~(ADC_CR2_SWSTART | ADC_CR2_DDS | ADC_CR2_DMA);
Fixed in trunk, will go in the 18.x release. Sorry for delay...
Giovanni