Distiller randomly omitting borders / reverse boxes

Hi all, we are setting newspaper advertisements in QuarkXpress but when they appear on the PDFd plate some borders or reverse boxes are being omitted. The problem seems to only affect advertisements with logos and appears to only happen with reverse boxes. It is a relatively new problem. We have been using the same system for a few years now. We are distilling through Acrobat Pro 7.0. Any advertisements created through another application (eg. Illustrator eps files) appear as normal. I am attaching a few examples. Any help would be appreciated.

1. Black Border missing:

2. Reverse box / logo at top and border missing.

3. Machinery Sales header should be on red box as 'Innisclan Road' header below