Toni,

We also have the Sakura film coverslipper and occassionally see this problem.  We see it on a lot of decals but also fairly often on prostate needle biopsies.  Are you using enough xylene on the coverslipper?  The brown area is where the film is not adhering tightly to the tissue and slide.  Try removing the tape and recoverslipping and I think the brown discoloration will go away.  If it doesn't help, try coverslipping by hand and see what happens.

Laurie Colbert