I don't now why you are getting muddy stains. What flux are you using? For SMD soldering I use a no-clean flux pen and solder paste, and I don't see any flux residues.
Maybe it's the solder paste? I use this no-clean paste: http://uk.farnell.com/jsp/search/productdetail.jsp?sku=876768. I store it in a sealed bag in the fridge, and warm it before use.