Question:

Why are these perpendicular angle marks being drawn as squares? I just want two lines.

Answer:

Although it is not obvious from your diagram, this is because you are drawing shaded angle marks and the shading has been set to white. When angle marks are shaded, they draw the complete square.

Here I have marked an angle as perpendicular and shaded it. In your case the shading is white but I have made it green so that you can see it. To get a normal perpendicular mark, select the angle mark (as shown above) and change the shading to none.

When there is no shading attached to the angle mark, FX draw will only draw the two lines rather than the square.