When my dock "hides" it takes other open windows with it

Hi,

Sometimes when my bottom (main?) dock auto-hides, it minimizes my open
windows as well.  I've tried different Positioning->Interaction
settings, but either the functionality isn't what I want, or I have the
minimization issue.

On a side note, what I would like for an Interaction setting is just
normal desktop Z-Order, so that the dock is behind an open window when
the dock loses focus.  I thought "Hide in background when not in use"
would of accomplished that; but when I have that selected I still find
the dock "hiding" at times.

Thanks in advance.