Hi to Rachel and histonet,
                                         I work with resin embedded soft
tissue with metal implants and I also had a brownish precipitate that
made reading the slide for measurements next to impossible.  Also had
cracking of the section sometimes no matter how fast I covered from
water.  The solution to the precipitate issue I use is a modified stain
I pick up at a workshop at NSH 2000. Workshop No. 13 entitled
Preparation and Methods for Undecalcified Bone sections. The workshop
was given by D. Brown and M.Hyten both of Eli Lilly & Co.  The stain is
a modified Toluidine Blue/ Basic Fuchsin.  This stains like an H&E for
me on soft tissue and should work for you on bone since the work shop
was for bone in plastic !  
I never was able to figure out what was causing the cracking !  Was it
the alcoholic stains ?  Are there any good aqueous hematoxylins ?  Any
help would be very much appreciated!
thanks 
evan
edessasau@acri.com