In TAppEncTop.cpp, there is the following problematic line setting the encoder's refRegionOffsetPresentFlag based on the configuration value.

m_acTEncTop[layer].setRefRegionOffsetPresentFlag( i, m_acLayerCfg[layer].m_refRegionOffsetPresentFlag );

This is incorrect, as the argument to the function is the array rather than the indexed boolean value inside the array. The array index "[i]" needs to be added to the argument:

m_acTEncTop[layer].setRefRegionOffsetPresentFlag( i, m_acLayerCfg[layer].m_refRegionOffsetPresentFlag[i] );