Well that's your issue. Flexi can't process the file correctly. That preview image doesn't have anything to do with the actual print data that is sent to the printer.
EPS is old and I don't recommend using it. You are probably using some complex shade or something and saving it as PDF correct? Flexi doesn't have the real Adobe PDF engine.
It's just something you have to live with if you use Flexi or Versaworks(doesn't have APPE either). And you can't use that HP on Versaworks, so it's already out of the question.
You would be better of with Onyx or Caldera which both have the real Adobe PDF engine that can handle those complex files with no problems.
And yes, that is why they cost significantly more money than Flexi.