|What AI version do you use? |
I suppose that Opacity 50% it's actually a simple overprints. It would be interesting to look at the scan and the original .ai file, and the eps that was printed of course.
Are you sure that while saving the eps a flattening was not disabled?
Don't know what about you, but i always try to flatter all the files manually (except some simple things that can be problemlos trusted to AI). A flattening algorithm in Illustrator is a certainly powerful, but once in a while i meet a buggy ones.
What can i say? check the file again through Distiller for example or another program.
Also this might help: http://www.ask.com/answers/662358521/help-with-corrupt-illustrator-file-needed?qsrc=14106 or search on other forums, read about this issue more.
I can only guess, even if everything was OK after the quark. Maybe something wrong with a RIP, but it could be provided..