We use Prinect for prepress workflow but there are many problems with versioning; calculation for number of plates for versioning is not ok (extra colors appear) and there are other problems.
Is there are good substitute for Prinect for prepress workflow?
Your printfiles contain extra colors if in versioning you have extra plates. Check your PDFs. I don't think change the prepress workflow switch just because of versioning issues is the best way to go timewise.
