Benson-
Thank you for your thoughtful response! I am pretty certain though that my problem is not coming from 2D objects mixing in with my extruded circles. One of the models I am working with consists of two extruded circles and one extruded rectangle, with no other 2D objects. Actually, the only workaround I have found for my problem so far is to manually draw the missing lines in the Edit Annotation mode of the Viewport!
I should have been more specific.... The lines that are missing in my isometric views are some of the extruded circle's sides. In other words, I have this 3D object that looks like a cylinder, which, when viewed obliquely, should have two lines parallel to its longitudinal axis, one on either side, representing the cylinder's width. In my viewports, one of these lines will be missing, but in the design layer, in a 3D view and rotated to an oblique viewing angle, the lines all appear properly.
Thanks again for your input.
Steve