If you use the second option to import your stack, luminance is processed separately (but simultaneously!) to your colouring (the Compose button will be lit green ). This means you are working mostly on the detail (luminance) until you hit the Color module where the final composite is made and youi'll see colour.
You will also be asked to check your coloring in the Wipe module (it now wipes two datasets in parallel).
For DSLRs and OSCs where no whitebalancing has been applpied, this gives a small boost to signal quality.
This behaviour is really a shortcut for launching the Compose module, loading the individual channels, doubling the green exposure vs blue and red and selecting for L + Synthetic L form RGB, RGB for the "L, RGB" parameter. The reason for the green exposure doubling is that a DSLR or OSC with a Bayer matrix has two green samples per 2x2 patch, versus just one sample for red and one for blue.
Be sure also to check out 1.6 which is stable and close to release. It comes with a heap of new features, optimisations and other goodies.
Hope this helps & wishing you clear skies!
EDIT: also, if you'd like some help processing one of your stacks, let me know!
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