A good way to clean your deck is to modify the ritual you use to prepare your crystals. A good grounding spell or ritual works well, it seems to release the stored energy. If the energy is particularly 'thick' or negative, ground the deck and recharge it over the full moon. (You may need to use a different deck in the meantime.)
Check through your spell collection and find one that has worked for cleansing other things and give it try. Spells and rituals should always be open to change and growth. They share many elements in common so they are readily adaptable to your needs.
~Maat's Book of Shadows