I have been trying out some fibre based paper in my printer and get scratches that run in the direction of the print head. I tried changing the platen gap (via the menu on the printer) to widest and this did not stop the scratching. I also tried loading the paper from the front.

I can run the same paper through my old (and cheap) Epson R200 and not get any scratching at all.

Has anyone made a print on fibre based paper with an Epson pro 3800?

I just received some samples of Innova FB paper and this does not scratch. It seems the 3800 printer does not like Permajet FB paper.

No problem with the Innova FibaPrint papers on my end. Scratching could be due to the paper buckling during the printing process. Based on my experience, it seems that the scratching you're seeing on the other paper is perhaps something specific to that paper ...