The is caused by a 72 dpi limitation in plotting from MacDraw II. All pen widths are rounded up to the nearest whole point size, so pens of .25 mm and .35 mm will both round to 1 point, and only one of the pens will be used when plotting.
This does not occur when using Claris CAD 1.0v3 or later, or when using the MacPlot Professional driver from Microspot.
To work around the problem, you should try one of two approaches:
1) Use colors to differentiate subtle changes in line width. Although all your plotter pens may actually be of the same color, indicate in the MacPlot driver Pen Info window that the .25 mm pen is red, and that the .35 mm pen is, say, blue. As you construct your illustration in MacDraw, color all the .35 mm lines in blue, and all the .25 mm lines in red. This will force the plotter driver to use a different pen.
2)Construct your document using line widths of whole-point increments.