Help!!! My Illustrator PS misinterpreted in Esko's Barco

Question

My question is specifically for print. Havent encountered something like this in video or Multimedia.
For print I work in Adobe Illustrator CS4, Freehand MX and Corel. I generate PS files for final output len files which are processed on Esko's Barco system (Bakstage Pilot & Backstage Edit). Freehand files work like a charm on the Barco workflow but my Adobe Illustrator CS4 PS files tend to split scans(images), converts strokes to fills and distorts trapping information. Transparencies / overprint knockout images underneath...etc
This happens in both CS3 and CS4. Can anyone help to get things right for my len files? I should think Adobe is always in liason with their partners on all their updates. There is no telling how much "Pricy" Polymer has found its way to the trash can. Can anyone, please, help? I love
Illustrator, in fact I enjoy it but when it comes to final outputting I feel like we will close shop soon.

Answer 1

Mario, this is a very helpful reply you have given.
The difference with your workflow that I see is that we generate scope files generated from the postscript. The downside is that Barco interprets/converts our postscript files into Illustrator 8.0 to generate a Scope PDF file.
What I think we need to do down here is to liaise with our Esco Dealers if we need an upgrade. Because obviously CS4 is a higher version to be interpreted by a lower version.
This is to say, I havetried using native files and it still wont read.
We will talk soon and I will also check if we can generate EPF files as opposed to scope