i have had this happen on a couple of occaisons with 2001.
It seems to be with planar xsecs.
One component in an assembly is just not there at all when you go to show the given xsec.
I have found by sketching the xsec works. If you just draw a line to replicat the plane through your model and offset this parallel to the plane you originally wanted to use. Strange thing is that in the instances i've seen an offset of zero maintains the original problem.
change the offset to say 0.1/0.05 which is usually ok for drawing purpose and the missing part xsec appears