I have this same problem when exporting to pdf. Some lines appear, but others disappear. They have been exported as in the thumbnail preview panel in the pdf, the lines are there! They just don't show in the large page... very strange. I am using data driven pages, does that make any difference?
Any one have any ideas?
I have just worked out how to solve this! Change the transparency to 1% and the lines export correctly! So strange ArcMap...