We had the same problem.  The xylene had nothing to do with it and thick and thin sections was one thing that we thought might be the problem.  But when I destained and restained the same slides they stained the way they were supposed to .  Finally we found that we had a problem with the wash stations of our 
sakura stainer.  We had someone from sakaura come out and work on the machine and the staining has returned to what it is supposed to be.  It seems when we have too many racks on the stainer this problem comes back intermitently, and sometimes we have to shut the machine down and turn it back on.  Not sure exactly why this happens but if we follow this course of action our slides are staining correctly.
 

Connie Grubaugh
Las Vegas Nv.
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