I am an urban entomologist working in the field of urban pest management. We deal with problems such as yours every day. Here are some fundamentals that may help you out. There are many small flies out there and proper identification can make a huge difference in finding the source. NOTE: the term fruit fly applies to pests of fruit in the field, the flies we get on the bananas are properly referred to as vinegar flies(Drosophilids). You can see examples of pest flies at the various extension entomology sites around the web. Drosophilids could breed in a decaying bathroom floor but there are some other flies that are more common in that situation. You would be well served by taking up the flooring at least in one spot to see what is going on down there.If you find nothing the search continues. Just because you haven't found it doesn't mean it isn't there. You will need to use your imagination to find them.