Dear Andy:

It is common to get a granular, brown precipitate (or at least it has the 
appearance of a precipitate) and sometimes glossy black nuclei in H&E stained 
sections when the sections are allowed to dry between the xylene and 
coverslipping steps.  I would suggest removing the coverslip and backing the 
slide up to absolute alcohol, or even 95% alcohol, and then re-clearing and 
coverslipping - taking care that the slides do not dry.

Freida Carson