Do you have the location of your pen table set in your config.pro? If not, it is not being used when you create the PDF. Here is what I have in my pen.pnt file that works fine for me:
! Pen 1 = white entities (object lines)
! Pen 2 = yellow entities (text, dimensions, cross hatching)
! Pen 3 = gray entities (hidden lines)
! Pen 4 = red entities (can use for drawing border if you change the
! entity color to red in the format file)
! Pen 5 = green entities (sheetmetal)
! Pen 6 = cyan entities (section)
! Pen 7 = dark gray entities (dimmed)
! Pen 8 = blue entities (spline surface grid)
pen 1 thickness 0.005 cm; color 0.0 0.0 0.0
pen 2 thickness 0.02 cm; color 0.0 0.0 0.0
pen 3 thickness 0.025 cm; color 0.0 0.0 0.0
pen 4 thickness 0.02 cm; color 0.0 0.0 0.0
pen 5 thickness 0.02 cm; color 0.0 0.0 0.0
pen 6 thickness 0.02 cm; color 0.0 0.0 0.0
pen 7 thickness 0.02 cm; color 0.0 0.0 0.0
pen 8 thickness 0.02 cm; color 0.0 0.0 0.0