Make a sketch with all desired walls and dimension the sketch. When a sketch is 100% dimensioned then the lines turn from white to green color. In the Arch workbench the walls will be built without gaps
Mike, at first welcome to the forum My guess is that you are working in the Part design workbench. In a body you do not need to join the shapes you made because Freecad sees a body as one solid. The Part workbench is different because there you need to do a boolean union of the different shapes you ...
My advice to prevent flipping is to change the dimensioning .
In this design I see a dimension "Width" of 38.1 mm and a "Thickness" of 3.175 mm.
Inroduce a Dimension Width-2 and let the spreadsheet calculate 38.1 - 3.175.
Now the Width-2 is a hard dimension and flipping of the 3.175 mm is not possible
In addition to the post of Chris I want to give the advice not to make the sketches to big. In situations like these I would split the sketch to 1 sketch for the outline and several sketches for the holes. These holes can be placed in the good position by using the "Create link to external geometry"...