Can you please post screen captures illustrating your problem?
- The contents of your atlas "Source model" in the Brainstorm window, and their view in 3D (as this tutorial: https://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas#Select_deep_structures)
- Right-click on the forward model > View lead field vectors > Follow the instructions to djust the display in order to see whether the arrows look similar in the left and right hemispheres => Screen capture
- The source results with the Amplitude slider set to 0%
- The MEG or EEG recordings time series, with the red cursor at the same time as the source maps
- All this both for the constrained and mixed models.
Note that we don't really recommend using this mixed models - see the warnings at the beginning of the tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/DeepAtlas