My smoker has plated, carbon steel racks.
If no skin present,and where the plating has worn, I will get carbon staining on the product.
Not the end of the world, but ugly.

I've never tried stainless steel racks...maybe that would help avoid the stain.

There are also smoking mats...like a synthetic mesh that might be the answer.

The best solution of course is to leave the skin on next time and smoke skin side down.
If your brine has a salty tendency, cut back on the salt or shorten the soak time.

Better yet, start using the "dry" brine method.
Here's one...
http://www.ifish.net/board/showthread.php?t=64066


The importance of establishing pellicle explained herein...
http://honest-food.net/2012/08/12/how-to-smoke-salmon-recipe/

Failing pellicle and temp control will yield cooked (not smoked) product, garnished with that fugly white curd (albumin).
Not fatal, but upper tier fugly.