Thanks for your reply. Here are updated test files proving the fault in the software using a fully updated Quark 2016 installation. I have highlighted in yellow the corrupted areas on the output PDF.
Previously Quark did fix some of the output corruption problem, but as you can see PDF output corruption remains in the current build.
This problem occurs, specifically, when Quark is set to Export Transparency Natively. This is the default for Quark 2016 and required for many workflows. This is a very bad bug, and I hope Quark will finish fixing it as quickly as possible.https://www.dropbox.com/s/1z7t9t3ujk05f ... s.zip?dl=0