Could you check, via phpMyAdmin, the products table and see if the Products with Sales/Specials are reflecting those amounts where the field:
products
products_price_sorter

are different ... as in the Sale/Special Price should be in the products_price_sorter ...

If the field:
products_price_sorter

does not contain the Sale/Special Price, do you import your products or manage them all manually in your Zen Cart Admin, as in you do not use Easy Populate or similar programs ...