I have done the following:
1) Under Products->Characteristics created two characteristics with multiple values
2) For two products I have added different characteristics
3) Created filters for the two characteristics with drop downs
4) Created a module to display the filters
When I select any of the pop-up values, the products displayed are the ones that have a characteristic of that type set irrespective of the value.
e.g. If the characteristic is colour and the product has 'red' set as a characteristic, selecting 'green' shows the product.
Multiple characteristics show no products even when there is a match.