I suspect contaminants in your waterbath OR in adhesives added to
waterbath.  I had a sample of waterbath adhesive sent to me (preopened!)
that had slime floating in the chrome subbing solution that was supposed to
be added to my waterbath.  Dumped that stuff!  

You did not say if you used waterbath adhesives, what kind of water
(distilled or tap)? 

Wash distilled water carboys (good Clorox wash, well rinsed) as green slimy
growth can occur, filamentous creatures from the deep, and do this on a
regular basis. Be careful with homemade tissue section adehsives, they can
be a source of floating things growing even after adding thymol crystals.   

Filter hematoxylin, and if you use the same source of distilled water to
rehydrate before hematoxylin, then hematoxylin could be getting a dose of
the same contaminant. 

Never had a paraffin create this problem

    
Gayle Callis
Veterinary Molecular Biology
Montana State University
Bozeman MT 59717-3610
406 994-4705
406 994-4303